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Objectives: To evaluate intermediate treatments between sodium hypochlorite and chlorhexidine gluconate irrigations for the prevention of a toxic brown precipitate in root canal therapy., Materials and Methods: Thirty-nine premolars were irrigated with 6% sodium hypochlorite and divided into either: No intermediate treatment; Dry paper points; three different irrigations with 17% ethylenediaminetetraacetic acid, deionized water, or 5% sodium thiosulfate. 2% chlorhexidine gluconate was the final irrigant in all groups. Sectioned teeth were analyzed for brown precipitate intensity and area using stereomicroscopy and components related to para-chloroaniline using Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS)., Results: Stereomicroscopy showed that 5% STS significantly reduced brown precipitate intensity and area as compared with no intermediate irrigation (p < .05, Chi-square, generalized linear model, and Tukey's multiple comparison tests). Utilizing ToF-SIMS, 5% sodium thiosulfate was most effective in reducing the components representing para-chloroaniline and chlorhexidine gluconate., Conclusion: The 5% sodium thiosulfate was most effective among other intermediate treatments, assessed by stereomicroscopy and ToF-SIMS., (© 2022 The Authors. Clinical and Experimental Dental Research published by John Wiley & Sons Ltd.)