BackgroundTo investigate the combinations of Musculoskeletal pain (MSP) (neck, shoulder, upper and low back pain) among a sample of Iranian school children.MethodsThe MSP combinations was modeled by latent class analysis (LCA) to find the clusters of high–risk individuals and multigroup LCA taking into account the gender and age (≤ 13 years and ≥ 14 years of age categories).ResultsThe lowest and highest prevalence of MSP was 14.2% (shoulder pain in boys aged ≥14 years) and 40.4% (low back pain in boys aged ≤13 years), respectively. The likelihood of synchronized neck and low back pain (9.4–17.7%) was highest, while synchronized shoulder and upper back pain (4.5–9.4%) had the lowest probability. The probability of pain at three and four locations was significantly lower in boys aged ≥14 years than in other gender–age categories. The LCA divided the children into minor, moderate, and major pain classes. The likelihood of shoulder and upper back pain in the major pain class was higher in boys than in girls, while the likelihood of neck pain in the moderate pain class and low back pain in the major pain class were higher in children aged ≥14 years than those aged ≤13 years. Gender–age specific clustering indicated a higher likelihood of experiencing major pain in children aged ≤13 years.ConclusionsThe findings highlight the importance of gender– and age–specific data for a more detailed understanding of the MSP combinations in children and adolescents, and identifying high-risk clusters in this regard.