In an open, prospective, randomized study, the efficacy of fluconazole was compared with that of the combination amphotericin B/flucytosine. Forty surgical patients with deep-seated mycoses were included in the study. Absolute inclusion criteria were histological finding of fungi in a tissue sample taken during surgery from e.g. peritoneum, pancreas, lungs or trachea, a positive blood culture or candida lesion of the eye. According to the random list 20 patients received up to 0.5 mg amphotericin B per kg body weight in combination with 3 x 2.5 g flucytosine (5-FC) daily and 20 patients received fluconazole, 400 mg on the first day and then 300 mg daily. The two therapy groups were comparable in terms of age, sex and underlying diseases. Gastrointestinal perforations (27 times) were the most frequent underlying diseases. Candida albicans was the fungus most frequently detected microbiologically (34 times). The pathogens were eliminated from 12 patients in the fluconazole group and 14 patients in the combination group. The median elimination time was 8.5 days in the fluconazole group and 5.5 days in the amphotericin B/5-FC group. Six patients died in the fluconazole group, whereas five patients died in the comparison group. Side effects which necessitated switching of therapy occurred twice in the combination group. In deep-seated candida mycoses, surgical patients receiving the combination therapy with amphotericin B/5-FC showed an earlier elimination than patients on monotherapy with fluconazole. With respect to cure rates there was no difference between these two regimens.