Background Sugar-sweetened drinks (SSDs) are known to be cariogenic, but this association has not been well investigated in population-based repeated cross-sectional studies in recent years. Therefore, this study examined whether SSD intake is associated with higher caries experience in 10- and 15-year-olds. Methods The study sample included participants from the Munich study centre of two birth cohorts with data on non-cavitated caries lesions (NCCL/S), caries experience (DMF/S index), overall caries burden (DMF + NCCL/S) and SSD intake. In total, 915 and 996 children were included from the 10- and 15-year follow-ups, respectively. Intake (g/day) of SSDs, comprising cola, lemonade, ice-tea, sport/energy drinks, fruit squashes and nectars, was calculated from food frequency questionnaires. For analyses, the SSD intake was converted into portions (250 ml/day). Multiple logistic regression and prospective analysis models were performed to test associations between SSD intake and various definitions of caries, adjusting for sex, parental education, body mass index (BMI) categories, study cohort, plaque-affected sextants, mode of SSD consumption, energy content of SSDs, and total energy intake. Results The mean overall caries burden at 10 and 15 years of age was 1.81 (SD: 2.71) and 6.04 (SD: 8.13), respectively. The average consumption of SSDs at the 10- and 15-year follow-ups was 0.48 (SD: 0.85) and 0.83 (SD 1.40) portions/day, respectively. After adjusting for confounders, in 10-year-olds, SSD intake was significantly associated with higher caries experience based on the indices DMF/S (adjusted odds ratio: 1.29; 95% CI: 1.06-1.57), NCCL/S (1.24; 1.03-1.49) and DMF + NCCL/S (1.27; 1.05-1.55). At the 15-year follow-up, SSD consumption was significantly associated with increased DMF/S index (1.12; 1.01-1.25) only. Prospective model associating 10-year SSD intake with 15-year caries experience was not significant. Conclusions SSD intake significantly increases the caries burden in 10-year-olds, with attenuated effects in 15-year-olds. To prevent caries, SSD consumption should be reduced, especially in children and adolescents.