The objective was to evaluate the clinical efficacy of chemomechanical preparation of the root canals with sodium hypochlorite and interappointment medication with calcium hydroxide in the control of root canal infection and healing of periapical lesions. Fifty teeth diagnosed with chronic apical periodontitis were randomly allocated to one of three treatments: Single visit (SV group, n = 20), calcium hydroxide for one week (CH group n = 18), or leaving the canal empty but sealed for one week (EC group, n = 12). Microbiological samples were taken to monitor the infection during treatment. Periapical healing was controlled radiographically following the change in the periapical index at 52 wk and analyzed using one-way ANOVA. All cases showed microbiological growth in the beginning of the treatment. After mechanical preparation and irrigation with sodium hypochlorite in the first appointment, 20 to 33% of the cases showed growth. At the second appointment 33% of the cases in the CH group revealed bacteria, whereas the EC group showed remarkably more culture positive cases (67%). Sodium hypochlorite was effective also at the second appointment and only two teeth remained culture positive. Only minor differences in periapical healing were observed between the treatment groups. However, bacterial growth at the second appointment had a significant negative impact on healing of the periapical lesion (p < 0.01). The present study indicates good clinical efficacy of sodium hypochlorite irrigation in the control of root canal infection. Calcium hydroxide dressing between the appointments did not show the expected effect in disinfection the root canal system and treatment outcome, indicating the need to develop more efficient inter-appointment dressings.