A character, generally the main character and a child or minor in age, is shown to have missing, dead or otherwise absent parents. Because there is still the need for an adult figure around, the character's grandparents fill in the void. Generally, there are no aunts or uncles in the picture.
The child may feature as a Heartwarming Orphan. When using this trope would interfere with the plot, you often get a World of No Grandparents.
This happens in real life as well. Compare Family Relationship Switcheroo, when the child is raised by grandparents but believes them to be their real parents.
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Anime and Manga
Pinako Rockbell of Fullmetal Alchemist raised her granddaughter, Winry, after the murder of the young girl's parents. This was immediately after the death of the mother of two neighborhood boys, Ed and Al Elric, and she ended up with all three. She seems to have done a good job, as all three are prodigies in their respective scientific fields.
Yugi's grandfather in Yu-Gi-Oh!. He does have a mother, but she got Brother Chucked quite quickly. Rebecca Hawkins, as well.
In One Piece, Luffy and Ace were watched over by their grandfather, Vice-Admiral Garp. Somewhat subverted in that Garp wasn't Ace's grandpa by blood, but actually adopted him upon the request of Ace's biological father. Garp still considered him his grandson anyway, even if adopted.
Naruto has Konohamaru, but curiously - there are lots of orphans, but grandparents appear much less often than parents.
Sasori ended up being raised by his grandmother Chiyo after his parents were killed in battle by Kakashi's father Sakumo when he was 6.
Arika Yumemiya from Mai Otome, and Grandma's sayings are quoted throughout the show.
Rei/Mars from Sailor Moon is raised by her maternal grandfather after her mom dies. In the Manga and Live action, her father Takashi is still around but she refuses to have anything to do with him because of his cold treatment of her Ill Girl mother Risa, not visiting her a single time until her death; he isn't mentioned in the anime. Her grandfather isn't mentioned in the live action (nor anyone else she may be living with) thus not using this trope.
Ushio from CLANNAD lives with her grandparents until she's five years old, because Tomoya sees her as a reminder of his wife Nagisa, who died giving birth to her, and can't handle the depression. Once she's five, however, they start rekindling their bond.
When first introduced, Yukito Tsukishiro from Cardcaptor Sakura, though as they're often said to be out of town, his grandparents are never seen. As Yukito is the "false form" of the magical being Yue, most of his background is actually false memories, including his grandparents. They simply don't exist.
In the manga Baby and Me, one of Takuya's classmates claims to live with her grandparents because her father and mother are famous and are overseas. Actually, it turns out that her grandparents are really her parents, and she's embarrassed about the fact, so she lies.
Renton in Eureka Seven was raised by his grandfather after his mother died in childbirth and his father Adrock sacrificed himself during the New Era Summer of Love when Renton was a young child. His uncle appears in one episode, however.
Yasutora "Chad" Sado from Bleach. Chad's parents died when he was a little boy, so he spent a good part of his life under the watch of a Mexican Cool Old Guy named Oscar Joaquin de la Rosa, whom he referred to as "abuelo" (Spanish for "grandfather"); it's not fully known if the "Abuelo" was his real grandpa, a distant relative or a mere family friend, but Chad considered him as his gramps for all that was worth.
Same goes to Toshiro Hitsugaya and Momo Hinamori, raised together in Rukongai by an old lady whom they both called grandmother.
In the original Gakuen Hetalia, Seychelles mentions that she used to live with an old man she referred to as "grandfather". Since she's a nation-tan, it's highly doubtful they're 100% relatives.
Also, the young Italies used to live with their grandfather Ancient Rome until his "death", then were taken in either by Austria and Hungary (Chibitalia) or Spain (Chibimano).
Since Kotetsu Kaburagi from Tiger & Bunny can't properly raise his daughter Kaede due to his superhero role and Kaede's mother Tomoe died of illness years ago, Kaede lives with her paternal grandmother (and her uncle Muramasa aka Kotetsu's older brother) instead and has no idea about his Secret Identity until the second half of the series.
Lunlun from Hana no Ko Lunlun, since mom died in childbirth and dad followed five years later. Also some of the people she helps, like a Spanish girl named Isabel and a Moroccan boy named Sayid.
Takeshi Sendoh from Hajime No Ippo. His mother died few after he was born (maybebecause of childbirth, but it's not specified), his father was a firefighter who died in the line of duty when Sendoh was around five years old. Hence why he was raised by his widowed grandmother, the owner of a small shop in Osaka's ward of Naniwa.
Mario and Masako Natsume from Mawaru-Penguindrum. unfortunately, they also were victims of their grandfather's abuse.
Shinobu Iijyuin from Haikara San Ga Tooru, since his father is a very high ranked military man stationed abroads and his mother was a German noblewoman who never was accepted by Japanese society, so she had to leave baby!Shinobu with the Iijyuin clan.
Mei from Arashino Yoru Ni is raised by his grandmother, as his biological mother was killed protecting him from Giro and his pack of wolves in the prologue.
Nice Guy Panther from Eyeshield 21 was raised by his grandmother whom had given him his treasured sweatband. She was also the one who provided him the money with her own savings to go to Japan. He desired to join the NFL so his grandmother would no longer have to work.
Misaki from Hana No Mizo Shiru was raised by his grandfather after his parents died in accident...for a few years, until he died, too. Then he's left in Kawabata's care, which doesn't really end well.
In Kotoura-san, after Haruka was disowned by her parents, it was implied she was raised by her grandfather Zenzou.
In one continuity, Legion of Super-Heroes' Luornu Durgo(Triad/Triplicate Girl/Duo Damsel) was raised by her grandmother, until she died and Luornu was sent to a mental hospital, due to her three selves not being emotionally identical. The grandmother was like this, as well, though she didn't reveal it to Luornu until shortly before she died.
According to the 2-disc DVD of Atlantis: The Lost Empire, Milo Thatch was supposedly raised by his late grandfather Thaddeus Thatch (whose best friend was apparently Preston Whitmore until Thaddeus "was laughed at and died a broken man") because his biological parents were both killed in a railway accident.
In The Land Before Time (sequels, that is), Littlefoot is raised by his grandparents. Although the end of the first movie implied it pretty clearly.
Possibly Wybie in Coraline—it's not spelled out, but we repeatedly hear his grandmother call him home and learn about her past with no mention of his parents.
Films — Live-Action
Masao in Takeshi Kitano's Kikujiro No Natsu is a boy who is raised by his grandmother. The plot involves his looking for his estranged mother during the summer vacation (and meeting an oddball surrogate father figure).
In Letters to Juliet, Charlie's parents died when he was young so he was raised by his grandmother, which explains why he was protective around her.
Heidi starts when the title character goes to live with her paternal grandfather. Her friend Peter is raised by both his mom and his blind grandma.
Peter Hartling's book Oma ("Grandma") is about an Cool Old Lady who takes in her 5-year-old grandson Karl aka Kalle after his parents die. They both have to deal with the loss and with the grandmother's ailing health.
In Les Misérables, Marius Pontmercy's grandfather takes him away from his father after his mother dies by threatening to disinherit him if his father raises him.
In Fire and Hemlock, Polly is raised by her grandmother from around thirteen, after both her mother and father send her away to avoid difficulty with their love interests, leaving Polly stranded and sick in the middle of a strange city. Granny flatly refuses to let Polly's mother take her back even when she offers.
In Doctrine of Labyrinths, Corbie was raised by her grandmother, who is implied to have died at some point before she meets Felix and Mildmay. Her parents remain shrouded in mystery as she never gives any information about her mother, and all she knows about her father is that he was probably a Ygressine sailor because she looks almost exactly like the Ygressine people about town.
The Changeover: The male lead, Sorenson Carlisle was originally raised by foster parents, but after suffering abuse at their hands, he managed to escape to his birth mother and grandmother's dwelling place.
In "The Sword Bearer", John is raised by his maternal grandmother after his mother dies in childbirth. His father is missing until late in the book, and didn't even know he had a child.
Captain Marco Ramius in The Hunt for Red October was raised by his grandmother since his father was off being the model Soviet hero, something that shamed Marco deeply.
In Banana Yoshimoto's Kitchen, Mikage Sakurai was raised by her grandmother. The plot starts when Mrs. Sakurai dies and Mikage moves in with a friend of her, Yuuichi.
The main character in Robert Bloch's "Floral Tribute" was raised by his grandmother until the authorities found out that she saw dead people and transferred him to an orphanage.
Prue, Piper, and Phoebe from Charmed were raised by their grandmother after their mother's death and father's abandonment.
Mako/Shinken Pink from Samurai Sentai Shinkenger was raised by her grandmother. Both her parents are actually still alive but her mother was crippled in the climatic fight of the last generation and was unable to train her daughter in the family traditions.
It's revealed in the first episode of The A-Team that Murdock's mother died when he was five years old. His father is never mentioned. He mentions both grandparents on occasion, and it's implied that they may have raised him.
Sookie Stackhouse and her brother Jason in True Blood were raised by their grandmother after their parents died in a flood.
Special Agent Seeley Booth from Bones was taken from an abusive alcoholic father and raised by his grandfather.
It's indicated Brennan was rescued from foster care by her grandfather, but there's later info that makes things fuzzy about this.
Thalia's character Marimar in the Soap Operaof the same name was raised by her grandparents in a cute little shack near the sea. Then, they died in a fire. Literally.
Actually a pretty standard upbringing in Soap Operas, if the hero/heroine is orphaned.
Gentro Kisaragi, a.k.a. Kamen Rider Fourze lives with his grandfather in the latter's motor shop after losing his parents at an early age.
A plot point in one episode of Stargate SG-1 is that Daniel's parents died—in front of him—when he was eight years old and his famous anthropologist grandfather didn't take him in. Adult Daniel is still a little bitter about that.
In the Sufjan Stevens song "Romulus", the narrator and his brother are left in grandpa's care by their mom, who they apparently don't see again until Grandpa's funeral many years later.
Chris Rock discusses this in his special Bigger and Blacker. He says that "if a kid calls his grandmama 'Mommy' and his mama 'Pam', he's going to jail".
Eric Donner, a sample character in ''Scion', was raised by his grandfather, as his father (the god Thor) wasn't part of his life and his mother died young from complications from delivering Eric. (It wasn't Death by Childbirth, as she lived for several years following the birth.)
Cara from Final Fantasy V is taken care of by her Grandfather Galuf after her parents' disappearance.
Relm of Final Fantasy VI. However, Strago is more of an adopted grandfather (it's not made entirely clear).
Chloe in Harvest Moon: Tree of Tranquility and Animal Parade is raised by her grandfather, Ramsey.
In Harvest Moon: Friends of Mineral Town and the female equivalent, May is raised by her grandfather Barley, though it's suggested in a couple of events that her mother is still alive. Also, Stu is raised by his sister, Elli, who appears to have been raised by their grandmother, Ellen.
Dead or Alive: Gen Fu is fighting to save the life of his granddaughter, whom he raised himself.
Subverted with Lyn from Rekka no Ken, since she came to live with her grandfather only when she was in her mid-late teens and had been living alone for a bit after her parents (and whole tribe) died. Played straighter with Canas's son Hugh from the prequel; he was raised by his grandmother Niime since his parents died protecting their village from a snowstorm.
In New Mystery of the Emblem, My Unit can have various backgrounds chosen by the player, such as being the child of a merchant or a noble house, or perhaps an orphan; however, this simply affects their base stats, and no matter what, circumstances force them to be raised by their grandfather, who trains them from a young age to be an Altean knight.
Mai Shiranui from Fatal Fury and The King of Fighters is hinted to have lived like this too, since her only mentioned relatives are her grandfather and trainer Hanzou and her dead grandmother. The hairpin that she wears is hinted to be a Tragic Keepsake from said grandma.
According to Mai and Takuma's intro conversation in KOF XIII, Hanzou Shiranui recently passed away. Takuma straightforwardly asks Mai if she and Andy are up for the challenge of keeping up with the Shiranui school of ninjitsu now that Hanzou is gone, and Mai calmly tells him not to worry since they're ready for it.
This seems to be the case for Blue and his sister Daisy in Pokémon Red and Blue, as their parents are never brought up, only their grandfather Professor Oak.
Gabriel Knight was raised by his paternal grandmother; his parents died when he was still a baby.
Kainé in NieR was raised by her grandmother following her parents' deaths.
Mars in Shining Wisdom is raised and trained to be a knight by his two grandparents after his father (a famous knight) succumbed to the poison inflicted on him in a great battle with a dragon.
In Little Busters, Kud's mother was a busy cosmonaut, so she was raised primarily by her grandparents.
The Tibbles from Arthur are raised by their grandmother.
Applejack, Apple Bloom and Big Macintosh from My Little Pony: Friendship Is Magic are under the care of Granny Smith. Granted, Granny Smith is a type of apple and may not necessarily reflect her actual relationship toward them, but considering her age, the trope applies. Possibly applies more to the elder siblings given Granny's ailing health, which may or may not include the early stages of dementia; Apple Bloom was probably raised more by her older siblings. Canon has yet to actually address the question of what happened to their parents.
Huey and Riley Freeman in The Boondocks. Various news reports and other official statements treat "Granddad" as if it were Robert Jebediah "Mr. Bitches" Freeman's actual first or middle name. Even he does it. Huey and Riley's parents are stated to be dead (Robert spent their inheritance on the house), the anime suggests they have no aunts or uncles, so he is the closest person left to take care of them.
According to this site, "6 million children live in grandparent and other relative headed households nationwide" in the United States.
It's not that hard to find this. In certain parts of the United States (and many parts of the world) where there is a strong emphasis on family, it's not uncommon for three generations to live in a house together (or at least live close to each other.) If the grandparents are of retirement age and both parents have full-time jobs, this is one of the better situations (it gives the grandparents something to do, it prevents the children from becoming latchkey kids, and it's usually cheaper than a nanny or babysitter.)
A very common occurrence in Russia, even when the parents are alive and well. Due to Values Dissonance, it's considered perfectly normal to leave bringing up the kid until the age of 7 or even higher to the grandmother.
A common phenomenon in China since the Great Opening Up. Many people headed East to work in the cities, leaving their children in the care of the grandparents. As a result, many Chinese children in rural areas in China are much closer to their grandparents than their parents.
Ted Bundy's mother gave birth to him at a young age, and he was raised as her brother rather then her son.
Professional wrestler Arn Anderson was raised by his grandparents, as his father took off when he was an infant and his mother was a screw-up who had enough trouble taking care of herself.
Was and is pretty common in pre-industrial societies, especially when the whole family works on a farm or hunter-gathering. The youngest child's mother may not be far away, though.