This study aimed to evaluate the air and water contamination level and to identify the microbes isolated from a rodent facility located at the Federal University of Uberlândia, Minas Gerais, Brazil. Colony forming units (CFU) per milliliter was used for monitoring water quantitatively; CFU per cubic meter was used for air monitoring. The isolated colonies were identified for qualitative monitoring. Due to absence of specific parameters for these facilities, the results were analyzed according to Brazilian and international standards, depending on which best suited each sample. The mean total number of microorganisms in water ranged from 0.015 ± 0.02 to 0.999 ± 0.91 CFU/mL. The number of microorganisms in air ranged from 9.1 ± 4.6 to 351.56 ± 158.2 CFU/m³. Forty-one microorganisms identified in the samples obtained from the rodent facility were potentially pathogenic or opportunistic for animals and humans (e.g., Corynebacterium spp.). We concluded that the water and air samples were contaminated with potentially pathogenic or opportunistic microorganisms that can harm rodents and humans. On the basis of our observations, specific sanitary standards suitable for these facilities should be developed for controlling microbial contamination, which will prevent zoonosis and ensure the reliability of scientific results obtained from animal experiments.