Preventive measures have dramatically decreased the prevalence of dental caries in children. However, risk factors for the disease in children living in low-prevalence areas remain elusive. In the present study we evaluated associations between dental caries, saliva levels of mutans streptococci and lactobacilli, and diet with special emphasis on the intake of fermentable carbohydrates and dairy products in 4-year-old children living in an area where the overall caries prevalence was low. Dietary intake was recorded in 234 infants as part of the Study of Infant Nutrition in Umeå, Sweden (SINUS). Of these the parents of 124 children gave consent to participate in a follow-up at 4 years of age. Dietary intake, height and weight, dental caries, oral hygiene, including tooth brushing habits, presence of plaque and gingival inflammation, fluoride habits and numbers of mutans streptococci and lactobacilli in saliva were recorded. Using multivariate stepwise logistic regression, caries experience was negatively associated with intake frequency of cheese (OR = 0.67; 95% CI = 0.44-0.98) and positively associated with the salivary level of mutans streptococci (OR = 1.57; 95% CI = 1.21-2.03). Caries experience was not correlated with intake frequency or amounts of carbohydrate-containing foods, with any other particular food, or with daily intake of energy, carbohydrate or any other macro- or micronutrient. We conclude that cheese intake may have a caries-protective effect in childhood populations where the overall caries prevalence and caries experience are low and the children are regularly exposed to fluoride from toothpaste.