Exophiala is a heterogeneous genus implicated in a variety of illnesses. The aim was to investigate the presence of Exophiala species in the gastrointestinal tract from a pediatric population. Strains from stool samples were isolated and identified by sequencing internal transcribed spacer region. Results showed a prevalence of 13% of Exophiala dermatitidis. This is the first report of E. dermatitidis in the gastrointestinal microbiota from a pediatric population in a Latin-American country.