Objective: To identify the types, food sources, and pattern of carbohydrates that significantly contribute to dental caries in Puerto Rican children. Methods: As part of an island-wide cross-sectional oral health study in 1,587 twelve-year-olds, diet intake was assessed in a representative subset (n = 801) with a 24-hour dietary recall. Carbohydrate intake was quantified using a computer-based diet analysis program. Caries was assessed using the National Institute of Dental and Craniofacial Research diagnostic criteria. Odds ratios were used to associate carbohydrate intake quartiles with caries, after controlling for important confounders. Results: A total of 723 subjects had complete data. Most were females (54%) and attended public schools (77%). The caries prevalence was 33%. The highest quartile intake for the following sugars significantly increased the odds of caries compared to the lowest quartile: total carbohydrates (OR = 1.93, 95% CI = 1.08-3.46), total sugars (OR = 1.88, 95% CI = 1.01-351), sucrose (OR = 2.05, 95% CI = 1.13-3.70), fructose (OR = 1.95, 95% CI = 1.05-3.62), and inositol (OR = 2.52, 95% CI = 1.38-4.63). The main food sources of these sugars were juices, including natural juices with no added sugars, and sweetened beverages. The odds of caries also increased significantly in children whose 10% of total energy intake was from total sugars (OR = 3.76, 95% CI = 1.03-13.7). Conclusion: After adjusting for important caries risk factors, total carbohydrates, total sugars, ≥10% kilocaloric energy from total sugars, and sucrose, fructose, and inositol intake significantly increased caries risk. Our findings can help raise awareness about the potential caries risk from the main sources of these sugars, natural fruit juices and sweetened beverages, which are consumed in great quantities in many societies.