Endodontic treatment consists in necrotic pulp removal, proper root canal preparation, and sealed obliteration. The effectiveness of treatment depends on careful root canal disinfection of existing bacteria. Modern endodontics recommends the use of a rubber dam, not only to protect the patient from endodontic instrument aspiration, but also to protect root canals from bacteria existing in saliva. The aim of the study is a comparison of root canal disinfection among patients treated with and without rubber dam protection. Endodontic treatient of 36 patients who came to the Department of Conservative Dentistry and Endodontics was performed. 36 teeth were qualified to the treatment. In 17 patients the whole treatment was done with rubber dam protection. In the other 19 (II group) the treated tooth was isolated only by cotton rolls. After chamber trepanation, and after chemo-mechanical root canal preparation, samples of root canal bacteria were taken. After 24h incubation, the density of bacterial suspension was checked using a spectrophotometer. In both groups of patients very similar results were obtained: a high density of bacterial suspension in samples taken before treatment, and a significantly lower density in samples taken after chemo-mechanical root canal preparation. In our research the use or lack of use of a rubber dam does not change the effectiveness of root canal disinfection.