Background: Substance use among college and university students predicts substance related problems in later life. Few studies on this phenomenon have been carried out in low income countries, and most focus on primary and secondary school students. This study therefore aimed to establish the prevalence and factors associated with drug use among university and college students in a low income country.Methods: Design: A descriptive cross-sectional survey using the Self-Administered WHO Model Core Questionnaire to collect information on use of various drugs among students in colleges and university campuses within Eldoret Municipality in Western Kenya. Setting: Four tertiary learning institutions in Eldoret Municipality were randomly selected for inclusion in the study- three tertiary level non-university institutions and one university campus. Subjects: Five hundred students who gave consent to participate in the study, 125 from each of the four participating institutions. The mean age was 22.9 years (18-32, s.d. 2.5), and males made up 52.2% of the sample.Results: Lifetime prevalence rate of any substance use was 69.8%, and none of the socio-demographic factors was significantly associated with this. Lifetime prevalence rate of alcohol use was 51.9%, and 97.6% of alcohol users had consumed alcohol in the week prior to the study. The prevalence rate of cigarette use was 42.8%, with males having statistically significantly higher rates than females (p < 0.05). Other substances used were cannabis (2%) and cocaine (0.6%). Among those who admitted to using substances, 75.1% were introduced by a friend while 23.5% were introduced by a relative other than a member of the nuclear family. Majority of those using substances wanted to relax (62.2%) or relieve stress (60.8%). Problems associated with alcohol use included quarrelling and fights, loss and damage to property, problems with parents, medical problems and unplanned unprotected sex.Conclusion: The prevalence of substance use among college and university students in Eldoret is high and causes significant physical and psychosocial problems in this population. A large proportion of those using alcohol reported serious adverse effects, raising the necessity of targeted interventions to reduce the risk of subsequent substance dependence and other deleterious consequences.