Diet is recognized as one of the most important factors affecting the equilibrium of the oral bacterial flora. Studies related to dental caries development have focused mainly on the effect of carbohydrates. In the present work, using swabbing coupled with an immuno-colony-blot assay, we followed the indigenous oral bacterial populations of BALB/c mice fed diets with different concentrations of sucrose, starch, proteins, lipids, vitamins, and minerals for a period of 14 days. The results indicate that although high-sucrose diet favored an increase of the proportion of S. faecalis, only variations in the protein and the starch concentrations significantly influenced the composition of the indigenous oral bacterial populations of BALB/c mice. With low-protein diets, the proportion of Lactobacillus murinus decreased, that of Streptococcus faecalis increased, while that of Staphylococcus aureus was relatively stable. A diet containing a high proportion of starch (65%) resulted in a significant increase in the population of S. faecalis, while that of S. aureus decreased proportionally. With the same diets used as in vitro culture media, growth of L. murinus was the fastest at high protein concentrations, while that of S. faecalis was not affected by the protein concentrations. These results indicate a direct effect of dietary protein content on the indigenous oral bacterial populations of BALB/c mice.