It is obviously known that the autopsy staff are under higher risk of infectious diseases than the other staff in the hospital. Inappropriate infrastructure and ventilation system installed in autopsy room could also increase such risk efficiently. The aim of this study is to determine the presence of pathogenic bacteria and fungi in the autopsy room air, investigate the factors affecting the presence and the number of colonies of these microorganisms, and determine the extent of occupational risk in such scope. The samples for the study were obtained from the autopsy room of Morgue Department of Turkish Council of Forensic Medicine. Samples were taken from the indoor air during, before and after autopsy by means of settle plates and air sampler in summer and spring seasons. Blood Agar and Sabouraud Dextrose Agar were used for isolation of bacteria and fungi, respectively. Fourteen bacterial and 26 fungal species were cultured from the autopsy room air. Most frequently isolated bacteria were coagulase negative staphylococcus, Micrococcus spp., Bacillus spp., and diphtheroid bacillus for the gram positive, and Acinetobacter spp., Proteus mirabilis, and Eschericia coli for the gram negative groups. Most frequently isolated fungi were Penicillium spp., Alternaria spp., and Aspergillus flavus. When data obtained in the spring and summer was evaluated, it was found that the number of bacteria and fungi colonies grown in samples that were taken by using both methods, was significantly higher at the time of the autopsy than those taken pre and post-autopsy sessions. It was also determined that the autopsy room air had been contaminated with bacteria in 4 of 38 study days and with fungi in 18 of 38 study days. This study could make a contribution not only in the training of autopsy personnel but also in detection of preventive measure to be taken against infections as well as to establish a common database for similar national and/or international research studies.