Background In 2016 the United Nation Relief and Work Agency for Palestine refugees in the Near East (UNRWA) commissioned a survey on oral health among 12-year-old students at UNRWA schools in five fields of operation (Jordan, Lebanon, Syria, Gaza Strip and West Bank), following World Health Organization guidelines. The survey aimed to determine the prevalence of dental caries and periodontal diseases among Palestine students attending UNRWA schools and how this has changed over time. Methods A two-stage stratified cluster sample design was used. For each Field of operation, the sample size was calculated based on 95% confidence level, 80% power and margin of error of 4%. Clinical examination was carried out by trained Field Oral Health services Officers (FOHSOs) from the 5 fields. Teeth presence and condition, gingival bleeding and calculus and the presence of dental sealants in occlusal surfaces of permanent molars were recorded. Behavior information of students/parents were collected using a questionnaire that was self-completed by the child/parent under supervision. Results were compared with those from a previous survey carried out in 2011 with the same methodology. Results In the two surveys the distributions of students who had caries experience in their permanent teeth were similar (73.1% in 2011 vs 72.8% in 2016, p = 0.83). In 2016 a significant increase of missing teeth ( p < 0.01) and sealants ( p < 0.01) was observed. Both surveys have identified behavioral determinants for dental caries, particularly dietary habits such as soft drinks consumption. Gingival health also showed statistical differences among the fields. Conclusions The prevalence of caries experience was very high in all fields and, with regard to main oral health indices, no trend of improvement was observed through 2011 and 2016. Surveys’ results advocates the need of a large-scale integrated preventive approach toward oral health and the emerging growth of Noncommunicable Diseases (NCDs), in line with the WHO recommendations.

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