The association between caries prevalence and clinical (presence of visible plaque in the labial surfaces of maxillary incisors), microbiological (salivary levels of mutans streptococci) and dietary variables was evaluated in 142 1.0- to 2.5-year-old children attending public day-care nurseries in the city of Piracicaba – São Paulo. A significant difference in caries prevalence was observed between those children with and without visible plaque (χ² = 12.08, p < 0.001). The mean ds (decayed surfaces) was significantly higher in children with visible plaque on the maxillary incisors than in children without it (p < 0.001). Mutans streptococci were detected in 114 (80.3%) of the children. A significantly higher caries prevalence was observed in children with high levels of mutans streptococci compared to children with low levels (χ² = 28.67, p < 0.001). The mean ds was significantly higher in children with levels of mutans streptococci greater than 50 CFU when compared to children with 0 CFU or 1–50 CFU of mutans streptococci (p < 0.05). Children who were either never breast-fed or only until 3 months exhibited a significantly higher caries prevalence than those breast-fed for a longer time (χ² = 4.11, p < 0.05). A significantly higher caries prevalence was also observed between children that used bottle containing milk with sucrose and cereal than children using bottle with milk with or without sucrose (χ² = 6.24, p < 0.05). Children who started to eat salty meals at or after 7 months of age showed a significant higher caries prevalence than children who started earlier (χ² = 10.30, p < 0.01). These data support the evidence of an association between caries prevalence in young children and mutans streptococci levels, clinical and dietary factors.