Introduction: The control of microorganisms present on the surfaces of the dental environment is a critical factor. Contamination from these pathogens can occur through direct or indirect contact between surfaces and clinical staff. Stopping cross infection in dental offices represents a great challenge for dentists and microbiologists. Objective: To compare the bacterial load of the dental units of the centers of the Ministry of Public Health, after the disinfection process, in the interval of attention from one patient to another; in the city of Cuenca, Ecuador. Materials and methods: It is a cross-sectional analytical observational study, which analyzes 12 surfaces from 3 centers of the Ministry of Public Health (MSP) in the city of Cuenca-Ecuador, selected at random. Results: Samples were isolated on 4 surfaces, each from 3 health centers; where 4 microorganisms were identified among them: Streptococcus viridans, Bacillus Subtilis, Yeasts and Staphylococcus coagulase negative, where the most prevalent was Bacillus subtilis. Conclusion: The cleaning protocols are deficient; it is recommended to carry out periodic controls on the quality of disinfection in public dental health care centers.