Objective To compare the disinfectant effects of calcium hydroxide and traditional formaldehyde and cresol(FC) on the intracanal medicament in infected single rooted teeth. Methods A total of 84 single rooted teeth with chronic apical periodontits were randomly selected for the disinfection with calcium hydroxide or FC in root canal after the root canals were cleared routinely. Samples were taken before and after root canal disinfection a week later. The number and species of bacteria in the root canal and the change of clinic signs and symptoms were observed. All the patients were followed up for one year. Results The number and species of bacteria in the root canal decreased significantly and there was significant difference between the two groups ( P 0.05). Conclusion Calcium hydroxide is an effective disinfectant in root canal therapy.