The aim of the present work was to evaluate an environmental monitoring program for clean rooms, or classified environments, involved in the filling and quality control of biological products produced by Butantan Institute, Sao Paulo, Brazil. This monitoring established the quantification, characterization and seasonality of the microorganisms in air and operators and, moreover, determined the alert and action limits. The total detectable microbial number showed some contrasts in installed air purification systems and in the operational impact on adopted procedures. The typical microbial population consisted of Staphylococcus sp, Micrococcus sp, Bacillus sp and Penicillium sp. The highest microorganism concentration occurred during summer and springtime. The established internal alert and action limits supported the operational procedures. Therefore, the environmental monitoring program is recommended for other laboratories involved in the production of vaccines, hyperimmune sera and biopharmaceuticals.