The antibacterial efficacy of intracanal medication with 2% chlorhexidine liquid (CHX) was assessed in teeth with apical periodontitis. Canals in 22 teeth were instrumented at the first session, medicated with CHX, and reaccessed after 7 to 15 days. Bacteriological samples were aspirated at the first and second sessions, before (1A, 2A) and after (1B, 2B) canal instrumentation. Viable bacterial counts were obtained by culture (CFU) and microscopy using vital dyes. Microscopic counts were higher than CFU counts. Consistently high CFU counts in 1A samples (mean, 2 x 10(5) microL(-1) canal volume) decreased significantly (p < 0.0001) in 1B samples, increased significantly (p < 0.04) in 2A samples, and decreased in 2B samples to the level of 1B samples. Proportions of negative cultures followed the pattern of CFU counts. Intracanal medication with CHX did not reduce the bacterial concentration. Bacterial counts expressed per microliter canal volume added information beyond the counts per tooth as expressed in previous studies.