A common problem with root canal failures is chronic inflammation at the apex caused by overfilling of root canal materials. Dentin filings have been suggested as an apical plug to create a biocompatible barrier between the filling material and the periapical tissue. Unfortunately residual organic material, such as pulp remnants or bacteria, still may be part of the filings. Dentin filings removed from the tooth, cleaned, and then used to form a barrier might serve as an effective barrier. The purpose of this study was to evaluate methods of cleaning dentin of organic debris. NaOCl, sodium dodecyl sulfate, and 1% Triton X-100 were used to treat dentin shavings and were evaluated by a micro bicinchoninic acid protein analysis assay. Two series of experiments were performed. One compared the effect of temperature while using phosphate-buffered saline as a control and the second compared exposure times. The percentage of protein extracted from dentin samples increased with temperature. Sodium hypochlorite at room temperature extracted 24.6%, NaOCl at 37 degrees C extracted 26.9%, and NaOCl at 70 degrees C extracted 33.9%. Only NaOCl at 37 degrees C and 70 degrees C showed statistically significant differences from phosphate-buffered saline at room temperature with p-values of 0.028 and 0.019, respectively. The exposure time series showed a difference between a phosphate-buffered saline solution and 6.25% NaOCl. NaOCl removed approximately 90% of protein compared with 60% for the phosphate-buffered saline. A 10-min exposure to 70 degrees C 6.25% NaOCl may be an efficient means of removing organic material from dentin shavings.