Background: Smoking tobacco is disproportionably common among HIV-infected patients in the highly active antiretroviral therapy (HAART) era. Methods: An observational cohort study of 300 HIV-positive patients receiving care between 1996 and 2005 examined the effect of smoking on pneumonia risk. Multivariable analyses assessed the association between smoking and pneumonia risk and identified independent predictors of pneumonia during the HAART era. Results: Current smoking was common (67%). Eighty-two patients (27%) experienced 119 pneumonia episodes during 2151 patient-years of follow-up, with 7.2 episodes/100 person-years among smokers and 2.9 episodes/100 person-years among non-smokers (unadjusted incidence rate ratio (IRR): 2.50 (95% CI: 1.58, 4.09). Adjustment for age and HIV RNA level resulted in an IRR of 1.77 (95% CI: 0.98, 3.21). No prior antiretroviral therapy use (P-value <0.001), higher HIV RNA level (P-value = 0.01), lower CD4 count (P-value = 0.01), younger age (P-value = 0.01), and alcohol use (P-value = 0.04) were independent predictors of pneumonia. HAART use decreased pneumonia risk (IRR 0.28, 95% CI: 0.18, 0.44). Conclusions: While HIV-positive smokers had over a 2-fold increase in the rate of pneumonia, the trend did not reach statistical significance in multivariable models. Clinical factors such as HAART, alcohol use and immunological status are important in pneumonia risk.