Abstract: The object of this research study was to investigate pupils` understanding and knowledge of sexually transmitted diseases including HIV/AIDS. The research was done on a sample of junior secondary school pupils with an average age of 15 in 8 junior secondary schools. The sample contained 205 pupils of which 88 were boys and 117 were girls. The pupils were of average and above average ability. These pupils were given a questionnaire consisting of 4 sections, namely formal knowledge (content) consisting of 20 multiple choice items based on the junior secondary school science syllabus; non-formal knowledge consisting of 20 statements on sources of information on STDs and HIV/AIDS; sexual behaviour consisting of 15 statements and attitudes towards STDs and HIV/AIDS consisting of 16 statements. An analysis of pupils` responses showed an understanding of STDs and HIV/AIDS content covered in the science syllabus. However, some children`s answers reflected a cultural influence (bias). Children were reluctant to answer some questions for fear of being noted to be actively involved in sexual activities. With regard to sources of information on STDs and HIV/AIDS, an analysis of pupils` responses showed that the major sources of information included teachers (science, guidance and counselling) Radio Botswana, Daily News and Posters in Labs. Pupils responded differently to statements on sexual behaviours, which reflect inconsistencies in their answers. Students` responses to attitudes towards STDs and HIV/AIDS reflect clearly an understanding of the consequences of engaging in unprotected sex. In conclusion, some suggestions and recommendations were made to help teachers with skills, knowledge and instructional strategies that will enable them to effectively teach controversial topics such as HIV/AIDS and sexuality.