This study aimed to determine whether enamel matrix derivative (Emdogain) affects the demineralization of bovine enamel in vitro and to assess the agent's anti-caries potential. Bovine enamel blocks were prepared and randomly divided into three groups (n = 15 per group), which were treated with distilled water (negative control), NaF (positive control), or Emdogain. All three groups were pH-cycled 12 times over 6 days. The percentage of surface enamel microhardness reduction (%SMHR), calcium demineralization rate (CDR), surface roughness, lesion depth and mineral loss after demineralization were examined. Surface morphology of specimens was studied by scanning electron microscopy. The Emdogain and positive control groups showed similar surface roughness, lesion depths and mineral loss, which were significantly lower than those in the negative control group. In addition, the enamel surfaces of both the Emdogain and NaF groups showed much narrower intercrystalline spaces than the surfaces of the negative control group, which exhibited extensive microfractures along the crystal edges. %SMHR differed significantly among all three groups, with the smallest value in the Emdogain group and the greatest in the negative control group. These results indicate that enamel matrix derivative (Emdogain) can significantly inhibit demineralization of bovine enamel in vitro, suggesting that it has potential as an anti-caries agent. SCANNING 36:194–201, 2014. © 2013 Wiley Periodicals, Inc.