Background: Substance use is rife in our society and adolescents (10-19 years) do face this problem during this vulnerable period of growth and development. Use of substances is known to be associated with poor health choices and risky sexual behaviour. Since the advent of antiretroviral therapy (ART), significant progress has been made with reduced rates of mother to child transmission (MTCT) and a general downward global trend in acquired immunodeficiency disease (AIDS) related mortalities. However, human immunodeficiency virus (HIV)/AIDS is still a leading cause of mortality in adolescents living in Sub Saharan Africa, with an upward trend in new HIV infections in adolescents. Limited information and research done on adolescents, makes them outliers in this epidemic. Objective: The purpose of this study was to determine factors associated with substance use among adolescents living with HIV in Kenya. Secondary objectives included determination of prevalence of substance use, association between substance use and reported adherence and association between reported adherence and viral load. Methods: A cross-sectional study was conducted among adolescents living with HIV attending Kenyatta National Hospital’s (KNH) and Gertrude’s Children Hospital’s (GCH) comprehensive care clinics. Data were collected using an interviewer administered questionnaire. Chi-square test of independence was used to assess simple association between substance use and each of the component of the factors. Effects of the components items on substance use were assessed using logistic regression model. Results: A total of 336 adolescents were interviewed (204 in KNH and 132 in GCH). Factors associated with substance use were: unemployment (OR=6.26, 95% CI=1.22-32.13, p=0.028), feeling pressured to engage in activities one would otherwise not do (OR=4.06, 95%CI 1.31- 12.59, p=0.015) and having friends/ schoolmates who use substances (OR=6.78, 95% CI=1.61- 28.57, p=0.009). Thirty one adolescents reported using substances and prevalence was 9.23% with a positive association between reported adherence to ART and substance use (p=< 0.0001) Conclusion: Substance use and HIV co-exist in the adolescent population and peers have a significant influence on behaviour development of an adolescent. The high prevalence of substance use in this study warrants for appropriate interventions especially after screening for alcohol and drug use as provided for in the Kenya minimum package for adolescents. In addition, peer influence should be used positively to foster good behavior and barriers to ART adherence addressed.