Objective The aim of this study was to elucidate the side effects after combination therapy of peginterferon and ribavirin for Japanese patients with chronic hepatitis C. Methods Inclusion criteria were HCV-genotype 1b and serum HCV RNA level of > 100 KIU/ml. Six hundred and twelve patients were received combination therapy and enrolled in this non-randomized prospective cohort study. Patients were monitored until the discontinuation of combination therapy based on treatment-related side effects. The percentage of each medication actually taken during treatment was calculated. Results Sixty-eight patients were stopped the combination therapy due to side effects. The cumulative discontinuation rate due to side effects of therapy was 8.4% at 0.5 year and 14.9% at one year. Discontinuation rate due to side effects was high with statistically significant in the following cases: 1) patients 65 years, 2) patients who had diabetes. Sustained viral response (SVR) was 17.6% (12/68) in the discontinuation group. In the discontinuation group, when the percentage of both peginterferon and ribavirin actually taken during treatment was >= 60%, SVR was 31% (9/29). On the other hand, when the percentage of each medication actually taken during treatment was < 60%, SVR was 7.7% (3/39). In the discontinuation group, patients with adherence of > 60% to the total of scheduled dose tended to have a high SVR compared to those with <= 60% adherence to the total of scheduled dose. Conclusion In combination therapy, patient age and complications of patient are important factors contributing to the safety. In the discontinuation group, patients with adherence of > 60% to the total of scheduled dose tend to have a high SVR.