The objective of this study was to identify target microorganisms as indicators of environmental contamination. The study evaluates the main environmental aspects and epidemiological chain related to such agents. Microorganisms were selected through key information about microbiological characterization of health care facilities' solid waste and evaluation of risk of infection from discarded sharps. The form of evaluation proposed for criteria adopted in the selection of contamination indicators included prior submission of a structured questionnaire to a network of specialists from the Federal District of Brazil. The specialists' multidisciplinary background, including professionals from the health field and an environmental microbiologist, helped define environmental contamination indicators by consensus. Pathogens such as Mycobacterium tuberculosis and hepatitis A and B viruses were specifically identified as capable of environmental survival or resistance.