In the Boku no Ryousei Guyuu series:

V.1 - Boku no Ryousei Guyuu Shoukougun (Syndrome)
"Which do you like better, Yukino? Front or back?"

High school boy Yoh Yukino has a secret. He is intersex, which means he has both male and female genitalia. He has never made any friends in school and has always been alone, but Ichinomiya, the bad boy in his grade, finds out his secret.
As Ichinomiya's fingers play with his crotch, Yukino gets carried away and gives his virginity to him. Their relationship started with casual sex, but they are inexperienced and sweetly awkward with each other. When Ichinomiya tells him he's cute, Yukino's heart starts to waver...?
"I am a boy... or a girl...?"

V.2 - Boku no Ryousei Guyuu Seishuuki (Mechanism)
"You really love xxxx, don't ya?"
Yoh Yukino is a beautiful intersex school student, and he's dating his classmate Ichinomiya, a tough guy with a strong sex drive and a scary face. In school, Yukino meets fascinating honor student Tsuzuki, who tells him this secret and sexually abuses him. Yukino is upset, Ichinomiya burns with jealousy, and as a result, the two make passionate love. After a while, Yukino realizes the hasn't got his period. "I had never really given much thought to the idea of getting pregnant with a body like mine..."

V.3 - Kare no Ryousei Guyuu Dokusenyoku

V.4 - Kare no Ryousei Guyuu Maternity