Objective: To evaluate the caries status of a cohort of 3-year-old caries-free children from 2 kindergartens in Beijing in a period of 2 years by using Cariostat caries activity test and to assess the sensitivity and specificity of Cariostat score as a caries risk indicator for caries-free children. Methods: Totally 426 3-year-old caries-free children from 2 kindergartens in Beijing were recruited in the present study. Informed consents were obtained from the children's parents. Dental plaque samples of the children were collected and the Cariostat caries activity tests were conducted at baseline and once a year for 2 years. After two years, the caries status of the cohort children were re-evaluated and the caries incidences amongst children with high (2.0, 2.5, 3.0), medium (1.5) and low (1.0, 0.5, 0.0) levels of Cariostat scores were compared and analyzed. Results: Totally 864 3-year-old children from 2 kindergartens were screened before the study startedand 426 (49.3%) children were caries free. After 2-year follow-up, 312 out of 426 (73.2%) remained in the study. The overall caries incident rate was 46.5% (145/312). The caries incident rate of children with high level of Cariostat scores was 88.9% (88/99), while the caries incident rates of children with medium and low levels of Cariostat scores was 38.7% (36/93) and 17.5% (21/120), respectively. The sensitivity and specificity of the Cariostat test in assessing the caries risk of 3-year-old caries-free children in a period of 2 years were 60.7% and 93.4%, respectively. Conclusions Cariostat caries activity test can be used as an indicator to predict the caries risk of 3-year-old caries-free children. Comprehensive caries management could be conducted for children in kindergartens based on the caries risk assessment results of caries experience and the Cariostat score.