Objectives: Correct and consistent condom use remains an important public health intervention against the spread of Human Immunodeficiency Virus and other sexually transmitted infections. There is paucity of information on sexual behaviour of in-school adolescents in Uganda. We, therefore, used secondary data of the Uganda Global School-based Health Survey (UGSHS) conducted in 2003 to determine the prevalence and correlates of condom use at last sexual intercourse in urban areas of Uganda. Methods: A two-stage cluster sampling technique was used to obtain a representative sample. Altogether 1709 students participated in the survey in urban areas of whom 179 (14.9% of males, and 7.9% of females) had sexual intercourse within 12 months before the survey. Results: Overall 77.3% (79.7% of male, and 72.3% of female) adolescents used a condom at last sexual intercourse. Adolescents who drank alcohol and used drugs were 64% (OR=1.64, 95%CI 1.54, 1.75) and 68% (OR=1.68, 95%CI 1.56, 1.81) more likely to have used a condom, respectively. Meanwhile, adolescents who ever got drunk, and who reported to ever had 2 or more sex partners were 55% (OR=0.45, 95%CI 0.42, 0.48) and 35% (OR=0.65, 95%CI 0.62, 0.68) less likely to have used a condom compared to those who had never got drunk, and who ever had 1 sex partner, respectively. Finally, adolescents who reported receiving no parental supervision were 45% (OR=0.55, 95%CI 0.53, 0.58) less likely to have used a condom compared to those who reported receiving parental supervision. Conclusions: Parental supervision may be effective in promoting condom use among adolescents. Furthermore, drinking alcohol was associated with condom use probably due to peer pressure and easy access of condoms in drinking places as condoms are not actively promoted in schools. There is need for further research on how in-school adolescents could access condoms.