Not to subscribe to stereotypes or anything, but a lot of the novel centers around John and Owen as adolescent boys, and let's face it: adolescent boys have a reputation for being fascinated with sex. That said, they tend to harbor this fascination because they're thinking about it and not experiencing it, which earns this novel a rating of PG-13. We see a lot of sexual frustration and anticipation in A Prayer for Owen Meany, but we don't really witness the act (with the exception of the scene in which Mr. and Mrs. Brinker-Smith go at it in some kid's dorm room while Owen hides under the bed and Johnny hides in the closet. Still, it's not like they actually see anything).
John Irving does a great job of illustrating what it's like to be a young adolescent just starting to experience sexual curiosities. We watch both Owen and Johnny experience the embarrassment of an erection inspired by the wrong person at the most inopportune time possible; we witness their fascination as they unwrap and examine a condom (a.k.a. "beetleskin") up close for the first time; we watch both boys experience the excitement that comes out of their attraction to Hester (which strikes us as a little weird, we don't know about you), as well as their nervousness that she will injure their "doinks."
Even as John and Owen grow up, sex is always lurking there in the background but never becomes too explicit. John remains a virgin for life – he jokes that he can't even give his virginity away. Owen is a different story – we assume that he's sleeping with Hester, but even John admits that all we can do is speculate – we're never totally sure that they're doing it. Even if Owen and Hester have sex, Owen's attitude towards sex and sexuality stays pretty tame – he's horrified to think that John F. Kennedy may have had an affair with Marilyn Monroe, and he complains that people spend too much time thinking about sex. Maybe he's right. Sex always seems to be on the character's minds – they just don't do it nearly as often as they think about it.