We conducted a cross-sectional study with 208 HIV-uninfected and 188 HIV-infected women in Uganda and Zimbabwe to investigate differences in median CD4 counts. Absolute CD4 counts were determined by flow cytometry. Multivariate analyses were used to examine the association of country and HIV-infection status on CD4 counts. Median CD4 counts were significantly lower in Zimbabwe than in Uganda overall (649 and 783 cells/mm3, P = 0.009) and among HIV-infected women (470 and 614 cells/mm3, P = 0.003). In separate multivariable models, CD4 counts were significantly lower in Zimbabwe in HIV-uninfected (P = 0.014) and infected (P < 0.001) women, controlling for age, contraceptive method, education and living with partner status. In a model combining HIV-uninfected and infected women, there was no significant interaction between country and HIV infection status (P = 0.344), suggesting that the relationship between country and CD4 count was not significantly modified by HIV infection status. This study reinforces the importance of establishing country-specific reference CD4 levels as CD4 count continues to be used as a key biomarker in clinical decision-making for HIV-infected individuals in sub-Saharan Africa.