Objective: Cigarette smoking in South Africa decreased sharply since the early 1990s. Waterpipe smoking increased, especially among students. We estimate the prevalence of waterpipe and cigarette smoking and associated characteristics among university students in the Western Cape. Methods: An anonymous self-administered online questionnaire was sent to all registered students at 4 public Western Cape universities. The 4578 valid responses were weighted to represent the Western Cape's university student population. We present descriptive statistics and logistic regressions. Results: We found that 63% of Western Cape university students ever smoked waterpipe, 9.9% of students smoked waterpipe in the past 30 days and 17.7% of students smoked cigarettes in the past 30 days. Waterpipe smoking has a strong socialization aspect. Controlling for confounders, current waterpipe smoking is associated with alcohol consumption (positively), age (negatively), population group (mixed-race and Indian students smoke more), religion (Muslims smoke more), faculty (medical students smoke less), and spending money (positively). Current cigarette smoking is associated with similar covariates, but not with age. Conclusion: Waterpipe smoking in the Western Cape is widespread, but less than cigarette smoking. Because all tobacco products are harmful, the government has an obligation to impose appropriate regulatory measures to reduce waterpipe consumption.