Objective: Calculate gram-positive bacteria, gram-negative bacteria, and fungus, through the microbiological monitoring of the air, the environmental surfaces, and the hands of the cleaning staff in five Health Centres placed in the Department of Meta (Colombia) in 2007. Methods: The study was done in five diverse Health Centres, microbiologically diagnosed by taking samples in each area: horizontal surfaces before and after being applied the cleaning and decontamination protocol, on the Health Staffs hands (nurses, physicians, doctors...) before and after being cleaned; and in the air: critical and no-critical zones. Results: The third Health Centre had the highest level related to bacterial pollution on its critical zone and the fourth Health Centre had the highest level on fungal contamination. Inside the hospital, the areas with the maximum levels of microbial focus were Hospitalization, Urgencies, and Diagnosis. The study found remarkable statistic differences between the microbial charge before and after being the hands cleaned (p<0.05) and before and after being applied the cleaning and decontamination protocol of environmental surfaces. Conclusions: The study let us demonstrate that an appropriate training, supervision and monitoring of cleaning hands and sanitization of environmental surfaces can certify the decrease of the bacterial and fungal biomass, which are usually found on the Health Centres building.