Combination therapy of saquinavir (SQV) and ritonavir (RTV) seems to have a strong antiretroviral effect pharmacokinetically. The purpose of this study was to examine the effectiveness of combined therapy using SQV and RTV in patients previously treated with protease inhibitors (PIs) and to identify the factors compromising the response to such combination therapy. Nineteen HIV-infected Japanese patients participated in this trial between June 1997 and July 1998, and were monitored until November 1998. Patients were treated with SQV (400 mg twice daily) and RTV (300 or 400 mg twice daily). Among the 17 patients who continued such therapy for longer than 3 months, 6 were responders. Among nonresponders, the duration of PI therapy was longer and a higher frequency of preexisting PI resistance viral mutations was detected than in responders. No significant differences were found in previous use of reverse transcriptase inhibitor therapy, CD4+ and CD8+ T cell counts, viral load at baseline, and plasma concentrations of SQV and RTV between responders and nonresponders. Our results suggest that the response to SQV combined with RTV therapy is complicated by previous long-term treatment with PIs, probably owing to multiple PI resistance mutations. Even in patients with a PI-sensitive HIV genotype, however, resistance mutations can develop during therapy and abrogate the effect of high plasma SQV concentrations.