Contamination by microorganisms of active and inactive noncavitated lesions was analyzed by scanning electron microscopy. The sample comprised 10 active and 14 inactive smooth surface lesions and 5 sound tooth surfaces. The active lesions were obtained through an in situ model. The inactive lesions and the sound surfaces were obtained from extracted teeth. The samples were split and the two resulting halves were analyzed. The lesion areas were measured in order to compare bacterial contamination in active and inactive lesions. Microorganisms were detected within the enamel in all lesions studied (active and inactive). Sound teeth did not harbor bacteria with the exception of one half tooth where one rod was observed in the enamel. Great variation was observed in bacterial contamination in both active and inactive lesions. Microorganisms penetrated rather deeply into some active as well as into inactive lesions, reaching the dentin in 5 inactive lesions. Bacteria were present in the tubular and intertubular dentin. No difference was observed in the number of microorganisms per square millimeter in the active and inactive lesions (p > 0.05). Cocci and rods comprised 99% of the organisms, while filamentous and spiral bacteria were seldom present. Yeast-like microorganisms were found in inactive lesions. The presence of microorganisms in inactive as well as active noncavitated lesions shows that bacteria inside dental tissue (enamel and dentin) do not impede the arrestment of the caries process.