BackgroundScabies is a neglected tropical disease caused by the mite Sarcoptes scabiei that burrows under the skin. It is a major health problem in tropical areas, largely affecting children. Scabies is common and highly contagious and in schoolchildren spreads quite rapidly, due to overcrowding and close contact within the schools. This study aimed to determine the risk factors associated with scabies infestation among primary schoolchildren in Bashagard County, one of the low socio-economic areas in southeast of Iran.MethodsTo conduct this community-based, descriptive, and cross-sectional study, four primary schools were randomly selected in the Bashagard County. All students in these schools were selected and examined for scabies. Clinical examination and sociodemographic profile of students were assessed using a pre-tested structured questionnaire. Chi-square test, and binary logistic regression were used to analyse the factors associated with scabies infestation by SPSS version 21 software.ResultsOut of 480 studied schoolchildren, 15 cases of scabies with a prevalence of 3.1 % were observed. The frequency of infestation in males was 1.6 % and it was 4.7 % in females. Independent factors associated with a high risk of scabies infestation in unadjusted analysis were being student of grade 5–6 (cOR = 13.12, 95 % CI 2.92–58.89, p = 0.0001), low educational level of father (cOR = 4.37, 95 % CI 0.97–19.59, p = 0.036), low educational level of mother (cOR = 4.14, 95 % CI 1.92–18.57, p = 0.045), joblessness of father (cOR = 14.77, 95 % CI 4.97–43.89, p = 0.0001), employment of mother (cOR = 5.28, 95 % CI 1.38–20.16, p = 0.007), large family size (cOR = 3.34, 95 % CI 1.05–10.64, p = 0.031), use of shared articles (cOR = 33.37, 95 % CI 10.82–102.90, p = 0.0001), and absence of bathroom in the house (cOR = 11.77, 95 % CI 2.16–63.94, p = 0.0001).ConclusionsResults of this study confirmed that scabies is still one of the most important health problems in the primary schools of the Bashagard County. Low socioeconomic status and personal hygiene of the schoolchildren were the most important factors influencing the prevalence of scabies. Improvement of socioeconomic conditions and implementation of appropriate educational programs and active surveillance system to quickly detect and treat scabies cases are necessary in order to reduce the prevalence of scabies in schoolchildren in this area.