Objective: We aimed to study the long-term associations between sucrose intake (SI), selected representatives of the cariogenic oral flora, and the dental health of children from 3 to 16 years of age. Methods: At 7 months of age 1,062 infants (540 intervention; 522 controls) were included in the prospective, randomised STRIP-project aimed at restricting the child's saturated fat and cholesterol intake to prevent atherosclerosis when they become adults. At 3 years of age, every fifth child was invited (n = 178) to an oral sub-study, and 148 (78 boys) children attended. A restudy was conducted on 135 children aged 6, 127 aged 9, 114 aged 12 and 88 aged 16. SI using 4-day food records, plate-cultured mutans streptococci (MS), salivary lactobacilli (LB) and yeasts using commercial kits (Orion Diagnostica, Espoo Finland), toothbrushing frequency using fluoridated toothpaste and dental health expressed as d3mft/D3MFT were regularly recorded. Results: The SI of children whose intake was ≥10 E% (high SI) at 3 years remained high throughout the entire follow-up (p < 0.001, GLM for repeated measures) period, and they had higher salivary MS and LB counts (p = 0.024 and p = 0.068, respectively, GLM) than their counterparts whose SI was below 10 E% (low SI). No differences in toothbrushing habits were found between the high and low SI-groups. Caries-survival was strongly associated with low 6-year-counts of MS (p = 0.008, Cox regression analysis), and the d3mft/D3MFT-scores of the high SI-group were higher than those of the low SI-group (p = 0.046, GLM). Conclusions: High SI at 3 years was associated with high MS-counts (≥105 cfu/ml) and with a high risk for caries.