The pathogens of onychomycosis have implications in choosing therapy. We aimed to survey the pathogens of onychomycosis in Taiwan and further analyse the distribution of pathogens in various conditions. We also compared the distribution of pathogens in Taiwan with those in various countries. This study included 182 cases of onychomycosis who attended our clinic between January and December 2001. Histopathologic examination and fungus culture of the nail specimens were performed to confirm the diagnosis and identify the pathogens. The pathogens were dermatophytes in 101 patients (55.5%), Candida in 66 (36.3%), and non-dermatophyte moulds in 16 (8.2%). Candida was more frequently seen in patients older than 60 years (40.9%), females with fingernail onychomycosis (66.7%) or combined fingernail and toenail onychomycosis (58.3%), and presence of paronychia (57.9%). Dermatophytes are the predominant pathogens in temperate Western countries; meanwhile, Candida and non-dermatophyte moulds are prevailing in Mediterranean and tropical countries including Taiwan. Clinicians should appreciate that the pathogens of onychomycosis may vary in different patient groups and geographical locations, and choose optimal antifungal agents accordingly.