BACKGROUND/OBJECTIVES: There is an urgent need for effective interventions to improve the sexual and reproductive health of adolescents. Reliable data on the sexual health of adolescents are needed to guide the development of such interventions. The aim was to describe the sexual health of pupils in years 4 to 6 of 121 rural primary schools in north western Tanzania, before the implementation of an innovative sexual health intervention in 58 of the schools. METHODS: A cross sectional survey of primary school pupils in rural Tanzania was carried out. The study population comprised pupils registered in years 4 to 6 of 121 primary schools in 20 rural communities in 1998. Basic demographic information was collected from all pupils seen. Those born before 1 January 1985 (aged approximately 14 years and over) were invited to participate in the survey, and asked about their knowledge and attitudes towards sexual health issues, and their sexual experience. A urine specimen was requested and tested for HIV, Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and, for females, pregnancy. RESULTS: 9283 pupils born before 1 January 1985 were enrolled and provided demographic information and a urine sample. Male pupils were significantly older than females (mean age 15.5 years v 14.8 years, p<0.001), but all other demographic characteristics were similar between the sexes. 14 (0.2%) of the enrolled pupils (four male and 10 female) were HIV positive, 83 (0.9%) were positive for CT, and 12 (0.1%) for NG. 32 female pupils (0.8%) were positive by pregnancy test. Sexual experience was reported by one fifth of primary school girls, and by almost half of boys. Only 45/114 (39%) girls with biological markers of sexual activity reported having had sex. CONCLUSIONS: HIV, CT, NG, and pregnancy were present though at relatively low levels among pupils in years 4 to 6 of primary school. A high proportion of pupils with a biological marker of sexual activity denied ever having had sex. Alternative ways of collecting sensitive data about the sexual behaviour of school pupils should be explored.