This study presents the levels and possible sources of selected polycyclic aromatic hydrocarbons (PAHs) in surface sediments from the Napoleon Gulf and Murchison Bay of Lake Victoria. Sediment samples were extracted and cleaned up for PAHs using UNEP, 1992, and EPA method 3630C protocols. The analysis of sample extracts was carried out using a gas chromatograph coupled to a mass spectrometer. Fifteen congeners, mostly the high molecular weight PAHs (HPAHs) (4-6 rings) were detected. Total (∑) concentrations varied from 44.2 to 80.2 ng g-1 dry weight (d.w.) at the Napoleon Gulf, while those at the Murchison Bay ranged from 17.0 to 55.0 ng g-1 d.w. Statistical analysis showed no significant difference in the concentrations of PAHs among sites (p < 0.05, ANOVA). It was noted that the concentrations for most sampling sites were far below the lowest effect levels based on the Sediment Quality Guidelines, except for one station at the Napoleon Gulf. Principal component analysis and diagnostic ratios indicated that PAHs of combustion and petroleum origin were dominant and brought about mainly by atmospheric deposition.