Several western countries have reported increases of sexually transmitted diseases such as gonorrhea, syphilis and chlamydia since the mid-1990s, especially among teenagers 16-19 years old. We conducted a school-based survey to assess awareness and knowledge of STDs among students attending the 8th grade and above in Bremen and Bremerhaven, two cities in northern Germany. Between October and December 2011 students completed an anonymous questionnaire on awareness and knowledge of STDs in 8 different schools. To assess awareness of STDs, the students were asked to indicate which STDs they had heard of. Knowledge of STDs was assessed based on 4 general questions. Furthermore, comprehensive awareness of HPV was assessed based on 3 items. We assessed differences in HPV awareness and knowledge of STDs by key demographic variables such as age, gender and migrant background. A total of 1,148 students aged 12-20 years (response 28 %) completed the questionnaire. 31 % had a migrant background and 55 % were girls. Almost all students had heard of HIV/AIDS, but only 23 % of chlamydia and 13 % of HPV. Significantly more girls than boys had heard of HPV (18 vs. 8 %) and chlamydia (31 vs. 16 %). Generally, low levels of STD knowledge and awareness of HPV were observed. In multivariable analyses, age, gender, and ever having had sex were associated with both STD knowledge and awareness of HPV. HIV/AIDS remains the only sexually transmitted disease most students have heard of. Sex education at school needs to be broadened to include STDs other than HIV/AIDS.