Background Celiac disease (CD) emerged as a public health problem, and the disease prevalence varies among different races. The present study was designed to investigate the prevalence of CD using serological markers in apparently healthy schoolchildren in Irbid City, Jordan. Additionally, the effect of positive serology on height, weight and body mass index (BMI) was evaluated. Methods The study population consisted of 1985 children (1117 girls and 868 boys), age range was 5.5 to 9.5 years. Height and weight were measured and blood samples were collected from each individual. Serum samples were analyzed for IgA anti-tissue transglutaminase antibodies (tTG) using a commercial enzyme-linked immunosorbent assay (ELISA). tTG positive samples were further analyzed for IgA anti-endomysium antibodies (EmA) with a commercial ELISA. Samples confirmed positive with EmA were considered seropositive. Results Sixteen children were CD positive. The serological prevalence was estimated to be 1:124 (0.8%; 95% CI, 0.5% to 1.3%). Significant impact on growth (height) was found in seropositive children. When both sexes were individually analyzed, only boys showed height reduction. Furthermore, seropositive boys also had a significant weight reduction. Conclusion This study demonstrated that CD is prevalent among schoolchildren in Jordan. The seropositive children tend to have lower height, weight, and BMI than the seronegative group. These differences were significant only for boys. None of the participants is known to have CD prior to the study.