Two sets of teeth with apical periodontitis were collected at different geographic locations to study the identity of bacteria left in the root dentinal tubules. Root dentin of 20 of these teeth was cultured from three locations between pulp and cementum (A, B, and C). In addition dentin from eight teeth was examined histologically. Using the culturing technique bacteria were found in 77% of the dentin samples from set 1 (Amsterdam) and in 87.5% of the dentin samples from set 2 (Glasgow). At greater distance, in layer C, from the pulp bacteria were found in 62% (13 of 21) of the dentin samples. Twenty-three percent (3 of 13) of set 1 and 25% (2 of 8) of set 2 contained >50,000 colony-forming units/mg of dentin in layer C. In layers closer to the pulp higher numbers of anaerobic bacteria and Gram-positive rods were found, as well as a larger number of bacterial species. Histological sections showed bacterial penetration in dentinal tubules in 5 of 8 teeth. In the other three teeth where the colony-forming units/mg recovered was <10,000, no histological signs of tubule penetration was seen. It seems clear that, in more than half of the infected roots, bacteria are present in the deep dentin close to the cementum and that anaerobic culturing of dentin is more sensitive than histology to detect these bacteria.