Received: February 2017, Accepted: May 2017 Background: Dental caries is the most prevalent oral disease among children. The first permanent molar has been introduced as an index for predicting caries activity, and determining dental and oral health status and the groups most vulnerable to caries. Thus, the aim of this study was to determine the prevalence of caries in the first permanent molars among students of 7 and 12 years of age in Rafsanjan, Iran, in 2009-2010. Materials and Methods: This cross-sectional study was conducted on 360 students (girls and boys) in Rafsanjan. The participants were selected through multistage random sampling. Clinical examination for the diagnosis of caries was based on the World Health Organization (WHO) criteria. Data were collected through interviews and clinical examinations and analyzed using Mann-Whitney and chi-square tests. Results: The total mean decayed, missing, and filled teeth (DMFT) index of the sample was 1.66 ± 1.47 (1.78 ± 1.51 in boys and 1.51 ± 1.42 in girls) (P = 0.081). Mean DMFT was 1.79 ± 1.33 and 1.52 ± 1.56 in the 12 years and 7 years age groups, respectively (P = 0.029). The decayed teeth (DT), missing teeth (MT), and filled teeth (FT) in this index were 52.21%, 40.96%, 6.82%, respectively. The prevalence of caries free (CF) among the students was 34.7% (31.28% in boys and 37.57% in girls). A statistically significant difference was observed among the students in terms of gender and age (P < 0.05); CF was 43.24% in the 7 years age group and 24.57% in the 12 years age group. Conclusions: Considering the WHO criteria, the prevalence of caries and CF in the first permanent molars among students of 7 and 12 years of age in Rafsanjan was relatively favorable.