Introduction Oral health in students, as an important health-related subject, would be effective on their growth, self-confidence, socialization, learning ability, daily activities, and quality of life. The aim of this study was to evaluate the DMFT index of 12-year-old students in Gonabad and Bajistan and its relation with their personal and family factors.Methods An analytic-cross sectional study conducted among 1280 the students residing in the two desert districts of Iran in 2016. The required data including the subjects’ demographic and family factors as well as their oral health situation extracted from The National School Oral Health Program. The data entered in SPSS (20) and analyzed via Kruskal Wallis, Mann-Whitney, and logistic regression model.Findings Mean (SD) of the students’ DMFT was 1.47 (1.82). This index was calculated 0.98 (1.47) for boy students and 1.91 (1.98) for girl students (P<0.001). There were significant association between mean of the students’ DMFT and their residency location (P=0.015), birth rank (P=0.032), and level of education of their mothers (P=0.035).Conclusion According to the findings, attention to oral health in students, especially in girls, seems necessary. Increasing the knowledge and sensitivity of parents (especially mothers) concerning oral health of their children, especially their girls, the use of intermediate forces such healthcare providers in school and oral health technicians in health centers, and the implementation of preventive interventions such as fissure sealant, fluoride varnish Therapy, and use of sodium fluoride mouthwash by students would be effective for improving the oral health of students.