Onychomycosis is a common nail disorder resulting from the invasion of the nail plate by a dermatophyte, yeast or mould species and gives rise to some diverse clinical presentations. The purpose of the present study was to isolate and identify the causative fungi of onychomycosis in the population of Tehran, Iran. Nail samples from 504 patients with prediagnosis of onychomycosis during 2005 were examined both by direct microscopical observation of fungal elements in KOH preparations and in culture for the identification of the causative agent. All samples were inoculated on (i) Sabouraud dextrose agar (SDA, Merck), (ii) SDA with 5% chloramphenicol and cycloheximide in duplicate for dermatophyte and (iii) SDA with 5% chloramphenicol in triplicate for mould isolation. The criteria for the diagnosis of onychomycosis caused by non-dermatophytic moulds were based on microscopical observation of fungal elements, growth of the same mould in all triplicate culture and no growth of a dermatophyte or yeast in all the cultures. Of 504 cases examined, 216 (42.8%) were mycologically proven cases of onychomycosis (144 fingernails, 72 toenails). Among the positive results, dermatophytes were diagnosed in 46 (21.3%), yeasts in 129 (59.7%) and non-dermatophytic moulds in 41 (19%). Trichophyton mentagrophytes was the most common causative agent (n = 22), followed by Trichophyton rubrum (n = 13), Candida albicans (n = 42), Candida spp. (n = 56) and Aspergillus spp. (n = 21). Nearly half of the clinically suspected fungal nail infections are onychomycosis and yeast is responsible for most of the infections in Iran.