In this study, the antibacterial activity of the different antibacterial solutions using as root canal irrigant was compared in the teeth with pulpal necrosis and with periapical pathosis. Thirty root canals of incisors and premolars of 20 patients were used. Before and after the root canal preparation, two canal samples were obtained by a harvesting method using a sterile paper point in the first appointment. During the biomechanical preparation, both irrigant solutions were used for each tooth which were randomly divided into two groups. Last samples were also obtained before the root filling procedure. Samples obtained from the root canals were subjected to microbiologic processing, including anaerobic incubation on trypticase soy agar for 5 to 7 days. After counting of CFU on the plates, we concluded that both chlorhexidine gluconate and sodium hypochlorite were significantly effective to reduce the microorganisms in the teeth with necrotic pulp, periapical pathologies, or both, and could be used successfully as an irrigant solution.