The Automated Teller Machine (ATM) is used by millions of people as an alternative to gain time instead of using traditional banking systems in Brazil and ATMs are frequently localized in São Paulo city around the hospitals. However, ATMs might be potential devices for microbial accumulation and transmission in the community. The objective of the present study was to evaluate forty-two ATMs, in two hospital areas (A and B) in São Paulo city for the presence of pathogenic fungi and bacteria. Samples were collected from biometric surfaces of the devices with sterile cotton swabs soaked in the sterile physiologic saline and were cultured on selective agar for yeasts, filamentous fungi and bacteria in the period of January 2017 to March 2018. Complementary biochemical tests were applied to confirm the bacteria and the taxonomic identification of molds was performed considering the morphological characteristics by microscopic observation. Our results suggest that the biometric surfaces in ATMs is an important environmental source of microbes, once that the genera Staphylococcus was predominant in all agencies of both hospital areas (83.3%), following of Streptococcus spp. (57%) and Enterococcus spp. (50%). The group of Enterobacteriaceae (Gram negative bacilli) were most frequent in both areas studied (57%). Seven different fungi genera were isolated from ATMs in area A and B and yeasts were predominant in all samples collected (47%), comparing with filamentous fungi (23%). We conclude that biometric ATM surfaces play an important role in microbial transmission in hospital settings, and healthcare professionals should wash and disinfect their hands carefully before touching patients.