Determination of HIV-1 subtype may be important in the management of HIV infected individuals, particularly with regard to deciding the CD4 cell count at which to initiate ART. Non-B subtypes A and D are prevalent in Uganda and individuals infected with subtype D appear to have faster disease progression compared to those infected with subtype A. We examined the level of apoptosis in CD4+ T cells in a study cohort of volunteers infected with subtype A and D infection. Although the levels of apoptosis in the activated CD4+ cells significantly decreased with viral suppression, CD4+ apoptosis in individuals infected with subtype D were found to be significantly higher compared to those infected with subtype A prior to antiretroviral treatment. Surface expression of PD-1 on CD4 cells in subtype D was substantially higher compared to subtype A (p=0.03). This difference was not observed in the CD8 population (p>0.05). Our findings suggest that the infecting HIV subtypes exert an independent influence on the disease outcome in response to antiretroviral treatment.