The purpose of this study was to evaluate the effectiveness of various intermediate irrigants for the prevention of precipitate formed by the interaction of sodium hypochlorite and chlorhexidine. Sixty extracted single-rooted human teeth were decoronated, and the canals were instrumented. In the Group 1, canals were irrigated with 17% EDTA and 2.5% NaOCl followed by 2% CHX. In Group 2, 3 and 4, saline, 10% citric acid and 70% isopropyl alcohol were used as intermediate flushes between the last two irrigants. Teeth were sectioned longitudinally and subjected to stereomicroscopic examination. The samples in Group 1 and 2 showed orange-brown precipitate, concentrated more in the coronal and middle thirds, whereas Group 3 and 4 showed no evidence of precipitate. The thickness of the precipitate was measured using the Image Analysis System (Chroma System Pvt. Ltd, India). The interaction between NaOCl and CHX resulted in an insoluble neutral salt as a precipitate that can be prevented using citric acid and isopropyl as intermediate flushes.