The disappearance of traditional sex education during rites of passage in African societies has left many youth uncertain of where to look for information. Against this backcloth, the objectives of this study were to identify knowledge gaps amongst adolescents in Kenya regarding sexuality, HIV/AIDS and reproductive health. A thematic analysis was conducted of questions posed by 735 school youth aged 12-18 years from Meru and Kajiado Districts. Results show that many questions showed curiosity and anxiousness. Knowledge appeared to be fragmented and sometimes revealed misconceptions, which may put youth at risk. The raised themes differed by gender and age. Questions on saying no to sex, sexual violence and female circumcision were a great concern for girls. Boys were more concerned with managing boy-girl relationships, preventing STI/HIV infection, and condoms. Concern about transition to adulthood, sexuality, STI and HIV/AIDS, myths and misconceptions, and intergenerational communication cut across both genders. Older teens were more concerned with questions on boy-girl relationships, norms and values regarding sexuality, and STI. Younger teens (< 15 years) wanted to know about reproduction, saying no to sex, HIV/AIDS, condoms, sexual violence and female circumcision. Compounding these challenges was the lack of intergenerational communication. The study identified important knowledge and communication gaps in sexual and reproductive health among in-school adolescents in Kenya. There is a need for sex education interventions for different age groups and genders. These interventions should work with parents, teachers and health professionals.