A total of 257 stool specimens comprising 203 from diarrhoeal children and 54 asymptomatic controls were collected from patients attending different hospitals/clinics in Lagos and Ekpoma, Nigeria and were screened for fungal agents using standard methods. Of the total number screened, 165 (64.2%) patients had fungal agents in their stools. Of these, 157 (77.3%) patients had diarrhoea and 8 (14.8%) patients were asymptomatic. Of these total number of positive isolates, Candida albicans, C. tropicalis, C. pseudotropicalis, C. glabrata and C. parasilosis accounted for 59.4%, 30.9%, 5.0%, 3.0% and 1.8% in that order. Results revealed a significant relationship (p < 0.05) between fungi and incidence of diarrhoea in children. There was no significant relationship (p > 0.05) between the age group studied and the incidence of fungal diarrhoea in children. The sex of the children also showed no significant relationship (p > 0.05) with the incidence of fungal diarrhoea. Results have revealed the emergence of Candida species in cases of childhood diarrhoea in our environment.