Discharging their duties, doctors manning autopsy departments and forensic examiners contact infected biological objects and risk contracting infectious diseases. The risk they run is much higher than dangers faced by specialists involved in other aspects of forensic investigations. This study aimed to assess the effectiveness and quality of mechanized cleaning of autopsy tools in ultrasonic cleaners following standard operating procedures. We compared the results of sanitary and bacteriological examination of the said tools washed manually and mechanically, with the help of ultrasonic cleaners. McNemar’s test used in the context of processing of the data allowed revealing the frequency of change of the monitored indicators between the two groups. Mechanical cleaning minimizes direct contact with the tools, allows decontamination of items of complex geometry (including their hard-to-reach parts) without damaging them and ensures high quality of cleaning. With ultrasonic cleaners, mechanized cleaning significantly shortens the time needed to clean medical tools, eliminates the need to wash them manually without compromising their operability, and brings down the risk of workplace injuries and occupational morbidity.