When exploring the root canal flora, before and after treatment, it is crucial to eliminate bacteria from the tooth surface before entering the pulp. If not, bacteria from the surface might contaminate the root canal sample resulting in false information. When using molecular techniques, not only bacteria are to be eliminated but also DNA from bacteria to avoid contamination from the surface. The aim of the study was to examine if DNA from bacteria can be eliminated using a modified disinfection protocol. Samples from the tooth surface were taken from ten intact teeth stored in ethanol/ glycerol (50 % / 50 %) prior to the experiment. The teeth were sampled before and after cleaning the surface with H2O2 (30 %), NaOCl (3 %) and EDTA (0.5 M). Samples were taken from buccal, occlusal and lingual enamel and dentin surfaces. All samples were analyzed with polymerase chain reaction and culture. In a second experiment, ten teeth were placed in a bacterial solution containing Enterococcus faecalis for three days and sampled as above. No growth could be detected using the conventional culture technique from the post-wash samples. The results show that the teeth could not entirely become free from bacterial DNA using the performed cleaning routine as all samples were positive for bacterial DNA after cleaning. The average amount of detectable bacterial DNA was decreased with 95 % after the cleaning procedure. The results confirm reduction of bacterial DNA after cleaning, however, detectable bacterial DNA is still evident after disinfection.