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Background  Globally the number of children reaching school age is estimated to be 1.2 billion children (18 % of the world’s population) and rising. This study was therefore designed to determine the school health services available and its practices in primary schools in Ogun state, Western Nigeria.    Methods  The study was a comparative cross-sectional survey of private and public primary schools in Ogun state using a multi-stage sampling technique. Participants were interviewed using a structured, interviewer administered questionnaire and a checklist. Data collected was analyzed using the SPSS version 15.0.    Results  A total of 360 head teachers served as respondents for the study with the overall mean age of 45.7 ± 9.9 years. More than three quarters of the respondents in both groups could not correctly define the school health programme. There were no health personnel or a trained first aider in 86 (47.8 %) public and 110 (61.1 %) private schools but a nurse/midwife was present in 57 (31.7 %) and 27 (15.0 %) public and private schools. (χ 2  = 17.122, P = 0.002). In about 95 % of the schools, the teacher carried out routine inspection of the pupils while periodic medical examination for staff and pupils was carried out in only 13 (7.2 %) public and 31 (17.2 %) private schools (χ 2  = 8.398, P = 0.004). A sick bay/clinic was present in 26 (14.4 %) and 67 (37.2 %) public and private schools respectively (χ 2  = 24.371, P = 0.001). The practice of school health programme was dependent on the age (χ 2  = 12.53, P = 0.006) and the ethnicity of the respondents (χ 2  = 6.330, P = 0.042). Using multivariate analysis only one variable (type of school) was found to be a predictor of school health programme. (OR 4.55, CI 1.918–10.79).    Conclusion  The study concludes that the practice of the various components of school health services was poor but better in private primary schools in Nigeria. Routine inspection by teachers was the commonest form of health appraisal. This may suggest that more health personnel need to be employed to cater for the health of the school children in Nigeria and other similar developing countries.    Electronic supplementary material  The online version of this article (doi:10.1186/s13104-016-2006-6) contains supplementary material, which is available to authorized users.

School health services and its practice among public and private primary schools in Western Nigeria