The purpose of the present study was to evaluate the effect of Apis mellifera propolis collected from two regions of Brazil on caries development in desalivated rats. Ethanolic extracts of propolis (EEP) were prepared from crude propolis samples collected in Minas Gerais state (MG), southeastern Brazil, and Rio Grande do Sul state (RS), southern Brazil. The flavonoid composition of EEP was analyzed by high–performance thin–layer chromatography (HPTLC) and reversed–phase high–performance liquid chromatography (HPLC). For the animal study, 30 specific pathogen–free Wistar rats were infected with Streptococcus sobrinus 6715 and surgically desalivated. The rats were randomly divided into three groups which were treated with 80% ethanol (control), EEP from MG and EEP from RS. The animals were placed in a König–Höfer programmed feeder and received 17 meals of diet 2000 daily at hourly intervals. The solutions were applied on the rat molars (25 μl on molars of each quadrant) twice a day, by using graduate syringes. After 3 weeks, the animals were killed by CO2 asphyxiation. For microbial assessment, the left jaw was removed and sonicated in 154 mM NaCl solution. Dental caries was evaluated according to Larson’s modification of Keyes’ system. The HPTLC patterns and HPLC profiles demonstrated that both quality and quantity of flavonoid aglycones of EEP from MG were different compared to EEP from RS. In general, it is apparent that EEP from RS contained the highest concentrations of pinocembrin, chrysin, acacetin and galangin. The group of animals treated with EEP from RS showed the lowest smooth–surface and sulcal caries scores as well as less caries severity in smooth–surface and sulcal lesions, and these data were statistically different when compared with the control group. The group treated with EEP from MG only demonstrated a significant difference in the severity of sulcal lesions when compared to the control group. The percentage of S. sobrinus was lower in the groups treated with EEP, but did not differ statistically from the control group. The results showed that the cariostatic effect of propolis depends on its composition, and consequently the region of collection of propolis samples.