This study tries to assess the level of comprehensive knowledge of HIV/AIDS and the factors associated with it among in-school adolescents in eastern Ethiopia. The reason for this study is that there are more adolescents in school today, in Ethiopia, than ever before. This is a cross-sectional school-based study in which respondents were students attending regular school in 14 high schools located in 14 different districts of eastern Ethiopia. The proportion of in-school adolescents with comprehensive HIV/AIDS knowledge was computed and compared by sex. The study concludes that about a quarter of in-school adolescents had comprehensive HIV/AIDS knowledge. Furthermore, the study determined that although females students are highly vulnerable to HIV infection they were less likely to have comprehensive HIV/AIDS knoweldge. Thus, HIV/AIDS information, education, and communication activities need to be promoted in these high schools.