- Early on, when Kouta realizes that Nyu endured the cold damp surf to try and get him a sea shell to replace the one she broke.
- Kouta and Lucy's day at the zoo.
- Really, almost any scene (aside from the one where she murders Kouta's sister and father) with young Lucy and Kouta counts.
- Later on after hearing Kouta talk about his last moments when his little sister Kanae and seeing his sad face. Nyu cuts her hair and impersonates Kanae saying she forgives him in order to console him.
- Mayu has several as her backstory is revealed. One, when she reaches the beach and feels safe from her parents. Two, when she first meets Wanta. Three, when the bakery merchant gives Kouta and Yuka a birthday cake for her, and shortly after this, Wanta, having ditched his supposed true owner, comes scratching at the door of Maple House, having faithfully followed Mayu to their new home.
- Also, the scene where Mayu is running away from the police, afraid that they are going to send her back to her abusive parents, only to run into Kouta, Yuka and Nyu looking for her, and telling the police that she's part of their family.
- Nana, each time she tries a new food or realizes that she has a home at Maple House. Also when she sticks by Kurama during his bout with mental illness, when he tells her she was nothing but an experimental subject to him.
- Nana and Nyu's friendship. As much as Nana hates Lucy, she doesn't hold anything against Nyu.
- Kurama, when his love for his adoptive daughter Nana is so fierce, he kills Barbara, a vicious clone of his real daughter Mariko, to protect Nana.
Kurama: Nana is indispensable.
- But let us not sell the love he had for said real daughter short, as it's just as heartwarming and tearjerking. In the anime, they both die together, in each other's arms, with Kurama imagining a happy life together that could have been. In the manga, the same thing almost happens, but instead they both live through it and Mariko ends up with a different death.
- Also, Mariko and Nana actually bond over their mutual love for their father right before Mariko's death in the manga, with Mariko telling Nana to take care of Kurama before she commits her Heroic Sacrifice to stop Lucy.
- Nozomi, when she accepts the encouragement of Kouta and Yuka to keep on singing, and later, when she asserts herself to her worried and misguidedly overprotective father.
- Yuka, when she flees to the beach, believing Kouta loves Nyu more, only to have Kouta come to retrieve her, angry that she should worry him, and proving he loves her by his concern.
- Lucy, when she sings while healing the mortally wounded Kouta, knowing that doing so will cause her body to melt—and this is after he said he hated her for what she did to his family.
- Kouta, in the very last panel of the manga, as he smiles and sees that his daughter's playmates are somehow connected with Lucy and Nyu, possibly their reincarnations.
- The very last reunion between Kouta and Lucy, it's both a Tear Jerker and a Crowning Moment of Heartwarming in both versions.
- Manga: Kouta may be hateful and bitter about what Lucy did, but he's still willing to let her stay with them, on the condition to never kill again. When she accepts, he actually hugs her, even Taking the Bullet Kurama shot at her. Why? Because he still loves her. He might not willing for forgive Lucy because he doesn't want to dishonor his father and younger sister's deaths but he's more willing to endure that hatred just to be with her. Because he has faith on her. That took some serious guts to come up with such conclusion.
- Anime: Kouta is still unforgiving, but ends up openly admitting that he loves her, then a tearful Lucy kisses him before leaving.
- Mayu finding out that Bando is still alive in the last chapter despite being cut in half by Lucy the last time she saw him. Considering this is a series where Anyone Can Die even the protagonist, it was a relief to see a previously thought dead character turn out alive and well.
- Similarly, the survival of Anna Kakuzawa and the Agent.
- The ending to the chapter that explains Nozomi's backstory We see the cassette tape that her father broke earlier taped back together in a drawer
- Alicia and Barbara holding up the helicopter to prevent it from crushing Nousou, at the expense of having Lucy severely wound or kill (in Alicia's case) them. Even though it turns out that this act of love and loyalty was the result of the mind-control devices implanted in their heads and not out of any genuine emotion, it's still a very sweet moment. It even makes Nousou rethink his stance on Diclonii and the way he's treated them.
Heartwarming / Elfen Lied
When this series brings the worse of humanity as well as diclonius and silpeits on their darkest, one can't forget that this series also shows the best as well, regardless of the race: