This study aimed to determine the prevalence of yeast fungi in samples from the glans penis and prepuce of circumcised and uncircumcised children. Impression preparations were made on modified Dixon and Leeming-Notman agar without cycloheximide. The isolates were identified by morphological and physiological characteristics. The yeasts were detected in 32 (28.6%) of 112 children, 12 (18.2%) being among 66 circumcised and 20 (43.5%) among 46 uncircumcised children. The most common species was Malassezia globosa (40.6%) followed by, Malassezia furfur (31.3%), Malassezia slooffiae (15.6%), Candida albicans (6.3%), Candida tropicalis (3.1%) and Candida parapsilosis (3.1%). The colonization with yeasts, and especially lipophilic species was more frequently observed among uncircumcised versus circumcised children. While age was not found to be a factor (P > 0.05), circumcision was responsible for increasing the colonization rate by 4.8 times (95% CI: 1.6-14.5) (P < 0.01). The circumcision status was not found to effect the distribution of Malassezia spp.