There are limited data on the efficacy of alternative regimens for treating patients with pneumocystis pneumonia (PCP). We compared the efficacy of clindamycin-primaquine (C-P) with that of pentamidine as a second line treatment for PCP. Among 91 patients receiving trimethoprim-sulfamethoxazole (TMP-SMX) as a first-line treatment for PCP, 31 (34%) did not respond and 7 (8%) had adverse reactions. Fourteen patients received C-P and 9 received pentamidine as a second-line regimen because of treatment failure or an adverse reaction to TMP-SMX. The response rate of patients to C-P was higher than the response rate to pentamidine (9/14; 64% vs 1/9; 11%; P = 0.03).