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Background  Dental caries is one of the most preventable oral diseases among children in developing countries. This study aims to estimate the prevalence and severity of dental caries in the first permanent molar and analyze the related risk factors among sixth-grade students in São Tomé Island.    Methods  A cross-sectional study with a stratified cluster sampling method was conducted on 1855 sixth-grade school children, mainly aged 11 to 14 years old, from 10 schools in 6 regions of São Tomé Island, from April 17 to June 27, 2021. Dental caries examination was performed by using the CAST criteria (DMFT) index, and the self-administered questionnaires about family background, oral hygiene, and relevant behaviors were collected. Multivariable logistic regression was used to study risk factors related to dental caries of the first permanent molar, and all data analyses were done using SPSS version 25.    Results  The prevalence of dental caries in the first permanent molar was 68.79%, without significant difference between gender, age, residence, and whether only child or not. The mean Decayed, Missing, and Filled Teeth (DMFT) index and mean Decayed, Missing, and Filled Surface (DMFS) index were 1.751 ± 1.514 and 3.542 ± 3.941, respectively. The rate of filling teeth was 5.50%, and Pit and Fissure Sealant (PFS) rate was 2.21%. The overall prevalence and DMFT index of dental caries of permanent teeth was 76.01% and 2.753 ± 4.569, respectively. The results of logistic regression analysis indicated that the frequency of candy/chocolate consumption (OR = 1.095) and fair self-assessment of dental health (OR = 1.354) were significantly associated with dental caries ( P  < 0.05).    Conclusions  The high prevalence of dental caries in the first permanent molar was a public health issue among sixth-grade school children in São Tomé Island. The prevalence of dental caries, mean DMFT and DMFS scores were higher, while the rate of filling and PFS teeth were lower than the average score of other African countries. Thus, oral health education, implement oral health preaching to school children and their parents is crucial to prevent dental caries.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12903-021-01846-z.

Prevalence of dental caries in the first permanent molar and associated risk factors among sixth-grade students in São Tomé Island