See article Anime of the 2000s.
- ×××HOLiC
- Agatha Christie's Great Detectives Poirot and Marple
- Air Gear
- Animal Yokocho
- ARIA
- Ashita no Nadja
- Axis Powers Hetalia
- Azumanga Daioh (although the manga was made in 1999)
- Baccano!
- Battle Spirits Shonen Toppa Bashin
- The Beast Player Erin
- Beelzebub
- Binchou-tan
- Black Lagoon
- Bleach
- Blood+
- Casshern Sins
- Cat Soup
- Ceres, Celestial Legend (although the manga was made in 1996)
- Chobits
- Chrono Crusade (manga ran from 1998-2004)
- CLANNAD
- Claymore
- Code:Breaker (manga, not the anime which came out in 2012)
- Damekko Doubutsu
- D.Gray-Man
- D.N.Angel (manga began in 1997)
- Darker Than Black
- The Daughter of Twenty Faces
- DEAD Tube
- Death Note
- Digimon
- D-Live!!
- Duel Masters
- Elemental Gelade
- Elfen Lied
- Eureka Seven
- Eyeshield21
- Fairy Tail
- The Familiar of Zero
- Farewell, Beloved Falco
- Fate/stay night
- Fullmetal Alchemist
- Fullmetal Alchemist (2003 anime adaptation)
- Full Metal Panic!
- Galaxy Angel
- Gankutsuou
- Gate Keepers
- Get Backers
- Ghost in the Shell: Stand Alone Complex
- Ghost in the Shell Stand Alone Complex 2nd Gig
- Gintama
- Gunslinger Girl
- Hajime no Ippo (although the manga was made ten years prior)
- Hakoiri Devil Princess
- Happy Happy Clover
- Happy World!
- Hekikai No Aion
- Haruhi Suzumiya: Yamakan jumpstarting the Light Novel adaptation revolution.
- Hayate the Combat Butler
- Hell Girl (the manga was made in 1997)
- Hello Kitty: From Apple Forest to Parallel Town
- Hellsing
- Hunter × Hunter (although the anime began in 1999, the series gained its following in the 2000s)
- Husky and Medley
- Ikki Tousen
- InuYasha (the manga began in 1996)
- Iris Zero
- IS Otoko Demo Onna Demo Nai Sei
- Jewelpet
- /Jiu Jiu (first volume published in 2009)
- JoJo's Bizarre Adventure
- Jo Jos Bizarre Adventure Vento Aureo (ran in the late '90's, but is set in 2001)
- Jo Jos Bizarre Adventure Stone Ocean (2000-2003)
- Jo Jos Bizarre Adventure Steel Ball Run (2004-2011)
- KOn
- Kaleido Star
- Katekyō Hitman Reborn!
- Kengan Ashura
- Kitsune No Yomeiri
- Kurozuka
- Le Chevalier d'Eon
- Love Gene XX
- Love Hina (although the manga was made in 1998)
- Love Lab (the manga, not the anime which came out in 2013)
- Love Monster
- Love Pistols
- Lucky Star
- Lyrical Nanoha
- Mahou Sensei Negima!
- Mai-HiME
- Mai-Otome
- Manga Shakespeare
- Maria-sama ga Miteru
- Massugu ni Ikou
- Mazinkaiser
- Mazinger Angels
- Shin Mazinger
- Shin Mazinger Zero
- Super Robot Retsuden. Published in 2002
- Medaka Box
- Metropolis
- Midori Days
- Minami-ke
- Mobile Suit Gundam 00
- Mobile Suit Gundam SEED
- Mobile Suit Gundam SEED Destiny
- Monster (the manga ran 1994-2001; the anime ran 2004-2005)
- Moribito: Guardian of the Spirit
- My Hero (2008)
- Moteki
- Nana
- Narutaru (though the manga began in 1998)
- Naruto (although it actually began in 1999 and a one-shot was drawn in 1997, its first volume was released in 2000)
- Ojamajo Doremi (Even though it began in 1999, a majority of the series ran during this decade. The English dub of the first season also ran during this decade.)
- Onegai My Melody
- Ouran High School Host Club
- Oyako Club
- Pandalian (2004-2005)
- Pandora Hearts
- Pani Poni Dash!
- Paranoia Agent
- Petite Princess Yucie
- Please Teacher!
- Please Twins!
- Pretty Cure
- The Prince of Tennis (although the manga was made in 1999)
- Princess Tutu
- Psyren
- Queen's Blade
- Rave Master
- Re: Cutie Honey
- Rental Magica
- Rosario + Vampire
- Rozen Maiden
- Saint Seiya
- Saint Seiya: The Lost Canvas
- Saint Seiya Next Dimension
- Saiyuki
- Sakura no Ichiban!
- Samurai 7
- Sayonara, Zetsubou-Sensei
- School Days
- School Rumble
- Scrapped Princess
- Sea Princess Azuri
- Sekirei
- The Severing Crime Edge (the manga was released in 2009)
- Shakugan no Shana
- Shaman King
- SHUFFLE!
- Skip Beat!
- Soul Eater
- Spider Man Manga J
- Stratos 4
- Super Gals
- Sylvanian Families
- Tai Chi Chasers
- Tengen Toppa Gurren Lagann
- Tenjho Tenge
- To Love-Ru
- Toradora!
- Transformers
- Tsubasa -RESERVoir CHRoNiCLE-
- Ultra Maniac
- Vampire Knight
- Vandread
- Viper's Creed
- Voices of a Distant Star
- The Wallflower
- Wandering Son (manga, not the anime which came out in 2011)
- Warcraft: The Sunwell Trilogy (2005-2007)
- When They Cry
- Touhou
- Touhou Sangetsusei (2005 - 2012, 2016 - Ongoing)
- Touhou Bougetsushou (2007-2012)
- Umineko: When They Cry
- Witchblade
- Wolf's Rain
- World's End Harem
- The World of Narue
- Yakitate!! Japan
- Zatch Bell!
- Zentrix
