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The members of the genera Candida and Malassezia comprise opportunistic yeast with a natural habitat on the skin of humans and warm-blooded animals. This study aimed to compare the prevalence of these yeast fungi in samples from the glans penis and prepuce 3–5 min prior to circumcision and after 1-month follow-up by mycological examination. A total of 77 children aged between 0.01 and 13.0 years (mean age 5.8 ± 3.4) were included in the study. Impression preparations were made on modified Dixon and Leeming-Notman agars without cycloheximide. The isolates were identified by morphological, biochemical and physiological characteristics. The frequency of yeast colonisation was found to be significantly decreased from 11.7% to 1.3% following circumcision (P=0.008). The glans penis and prepuce were colonised with especially Candida albicans (50%) followed by Malassezia furfur (40%) and Malassezia sympodialis (10%). This study highlighted the potential medical benefits of circumcision as a significant factor decreasing the colonisation rate of yeast fungi. We suggest that circumcision, rather than age, plays an important part in the reduction of yeast fungi in genitalia.