The purpose of this study was to evaluate the ability of gray and white ProRoot MTA to seal furcation perforations in mandibular molars using a dye extraction leakage model. Sixty-four mandibular molars were randomly divided into four experimental groups. Six teeth with perforations were used as positive controls and six teeth without perforations were used as negative controls. Perforations in groups 1 and 2 were repaired with white MTA. Groups 3 and 4 were repaired with gray MTA. Dye leakage was tested from an orthograde direction (groups 1 and 3) and a retrograde direction (groups 2 and 4). After dye extraction, absorbance was measured on a spectrophotometer at 550 nm. No statistically significant difference in leakage was found between gray and white MTA when used as a furcation perforation repair material. However, there was significantly more leakage when the perforations were challenged from the orthograde than the retrograde direction (p < 0.001).