The backstory of the Eli character is that ze was born a beautiful boy named Elias to a peasant family in the 1700s, and ze looked like a younger version of hir mother. There was an evil lord who liked young boys and ordered all the families to bring their boys to him so that he could pick his favorites. Elias was unlucky enough to be chosen. The lord castrated hir for his own sadistic pleasure, and then made Elias into a vampire. Elias was forced to abandon his family (although, the user bore posed the interesting theory that ze ended up eating them). By the time we meet hir in 1982, ze goes by Eli and apparently presents as female.
...It's not exactly clear if this is intentional. Eli is supposed to be very pretty anyway, so it could be that people just mistake hir as female and ze usually doesn't bother to correct them. Eli does notably say "I'm not a girl". However, when Oskar then asks if ze's male, ze says "No, no . . . I'm nothing. Not a child. Not old. Not a boy. Not a girl. Nothing".
So, Eli views hirself as outside all normal categories including gender. This might make hir genderqueer for the purpose of analysis from a modern LGBT perspective. Eli, in fact, never asserts a gender identity beyond stating what ze is not. In the original Swedish, the only gendered pronouns to describe Eli in the third-person narrative come from Oskar's perception of his friend's gender. A similar thing is done in the English version, but due to English's lack of gender-neutral pronouns, Eli is referred to as female outside of Oskar's perspective where it was otherwise neutral.
The book's author, John Ajvide Lindqvist, has posted on the "We, the Infected" forums a bit. In one post, he clears up some of his intentions with the Eli character:
I knew from the beginning that Eli was a boy. What happened when I let Eli meet Oskar was that Eli started to change his behaviour from what I had originally envisioned. I didn´t even know that they were going to fall in love. But I felt that Eli/Elias would try to appear more likeable in order to ge closer to Oskar, once he had decided not to kill him (The stroke on the cheek). Since Oskar percieves Eli as a girl, Eli is content with not informing him otherwise, although he can´t help himself on a few occasions. Eli doesn´t want to fool Oskar, he is uncertain if Oskar is going to leave him if the truth comes outHe adds:
Also, I tend to be interested in androgyneous (that word!) characters, and Eli was my first one. I wanted Eli to act as an in-between. Girlish sometimes, boyish sometimes. He can be anything, and he suprised me many times while writing the novel.So, as far as the author sees the character, Eli is male but androgynous (correct spelling) and can act either feminine or masculine. One example of this is after Eli mindmelds with Oskar, showing him very firmly that ze is not a girl, and ze then takes one of Oskar's mom's old dresses to change into instead of some of Oskar's clothes (ze got hir other clothes all bloody).
Lindqvist ends his post by saying:
But from the beginning Eli was just Eli. Nothing. Anything. And he is still a mystery to me.Yes, nothing is associated with everything. In Harry Potter, for instance, a vanished object goes nowhere and thus becomes a part of everything. In Let the Right One In, Eli views hirself as "nothing" in hir depressed vampire way, but "nothing" can mean "anything" in a more hopeful outlook. At the end of the book, Oskar smuggles Eli onto a train by keeping hir in a big suitcase. When the ticket-taker questions what's inside it, he says "a little bit of everything".
That's the novel. In the film, Eli is played by the very feminine Lina Leandersson, and all there is to show that Eli is androgynous is the line "I'm not a girl" and a brief shot of hir scarred crotch area. The line "I'm not a girl" isn't elaborated on, so the viewer can come to any conclusion as to its meaning, including "I'm a vampire" and "I'm an old woman". The crotch shot is very brief, and the fact that it's included at all is jarring, so it's easy to not understand the point of the shot. Oskar's only reaction to the glimpse is to widen his eyes, which could just be the reaction of a 12-year-old boy seeing his girlfriend's genitalia, and not 'OMG, my girlfriend's a castrated boy'. The film can easily be viewed without the viewer realizing there's anything unusual with Eli's gender. In fact, that's what happened with me. It took Internet browsing to learn Eli's not the cis girl ze appears.
In the forums, the user babyboi102909 has made the suggestion that book Eli is supposed to be a trans girl, that hir femininity and feminine presentation is evidence of a female gender identity. I am inclined to disagree due to the author's comments on the matter. Lindqvist likes androgyny, and Eli's femininity is just an expression of hir androgynous personality. However, the user Ingenting-ing has also made the interesting suggestion that film Eli can be thought of as a trans girl due to the actress' feminine portrayal. Having come from the perspective of initially viewing hir as a girl, I'm inclined to agree insofar as it's accepted as artistic reinterpretation and not the creators' intent.
The American remake Let Me In basically annihilates all queerness from the story. The line "I'm not a girl" is kept in, and Eli's American counterpart Abby elaborates that ze's "nothing" but doesn't touch gender. The crotch shot was removed, but Oskar's counterpart Owen is shown having a surprised reaction to peeking on Abby. Without the context, the only interpretation is that he's just surprised to see his girlfriend naked. A deleted scene shows Abby being attacked by hir sire, in which Abby appears feminine. Actress Chloe Moretz describes in an interview how director Matt Reeves had her write a diary from the perspective of the Abby character, and she wrote about Abby being turned by her creepy uncle. While unlikely to be canon, it shows a definite ignorance of the novel Let the Right One In. In an interview, Lindqvist complains that when he was consulted to shorten the title, "Let Her In" was the suggestion, showing that the androgyny of the Eli character was not well known by the American creators. Well, Matt Reeves does mention it in the audio commentary, but only in regard to how the peeking scene went in the Swedish version.
So, that's the low down on Eli and hir gender. In the novel, Eli came from the poor castrated boy Elias, and after which became a more androgynous person. In the film, Eli's background is only briefly brushed upon, and actress Lina Leandersson makes it easy enough to believe Eli is all girl if you aren't quick enough to catch the implications. In the American remake, Abby seems pretty clearly a cis girl. What exists as hints to Eli's true nature in the Swedish film are turned into what are more like references to the original film. Why, Eli truly is "a little bit of everything".