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Introduction Insects have been described as mechanical vectors of nosocomial infections. Methods Non-biting flying insects were collected inside a pediatric ward and neonatal-intensive care unit (ICU) of a Brazilian tertiary hospital. Results Most (86.4%) of them were found to carry one or more species of bacteria on their external surfaces. The bacteria isolated were Gram-positive bacilli (68.2%) or cocci (40.9%), and Gram-negative bacilli (18.2%). Conclusions Insects collected inside a hospital were carrying pathogenic bacteria; therefore, one must consider the possibility they may act as mechanical vectors of infections, in especially for debilitated or immune-compromised patients in the hospital environments where the insects were collected.