The lymphocyte profile of 521 HIV-infected subjects hospitalized at Jackson Memorial (2001–2002) was compared across main respiratory diseases. Study data included medical history and all laboratory evaluations performed during hospitalization. Community-acquired pneumonias (CAP, 52%), Pneumocystis jiroveci pneumonia (PCP, 24%), tuberculosis (TB, 9%) and non-tuberculous mycobacterial diseases (NTM, 12%) were the most frequent causes of admission. Patients hospitalized with PCP and NTM exhibited the lowest CD4 counts (P=0·003). PCP patients had the highest B-cell percentages (P=0·04). CAP patients had the highest CD8 and CD4 percentages and the lowest percentage of Natural Killer (NK) cells and viral burdens. TB patients exhibited the lowest NK-cell (11·4±6·3) and B-cell percentages (13·6±12) and the highest CD8 (59±14) percentage. NTM patients, in contrast, had the highest NK-cell percentages of the groups (19·1±11·6, P=0·01). Additionally, immune responses associated with respiratory pathogens differed in HIV-infected patients with CD4+ cells above and below 200 counts.