We estimated the prevalence of anemia among school children and investigated factors associated with this problem in Kuwait. A cross-sectional study was conducted on 1415 adolescents randomly selected from middle schools in Kuwait. Hemoglobin, iron, ferritin, folate and vitamin B12, in addition to many other laboratory indicators, were measured in a venous blood sample. Data on risk factors for anemia were collected from parents and adolescents. Multiple logistic regression was used to investigate factors associated with anemia. The prevalence of anemia was 8.06% (95% CI: 6.69-9.60%), which was significantly higher among females compared to males (10.96% vs. 5.04%; p < 0.001). Mean (SD) Hb level was 133.7 (9.89) g/L and 130.00 (10.48) g/L among males and females, respectively (p < 0.001). The prevalence of mild, moderate and severe anemia was 5.94%, 1.91% and 0.21%, respectively. Gender, age, iron concentration and ferritin were associated with anemia in multivariable analysis. These data indicate that anemia among school children in Kuwait is of mild public health significance. Further reduction in anemia in school girls should focus on correcting iron deficiency. Surveillance systems for anemia may consider using a cut-off point that is specific for the method of blood sampling and the method of Hb measurement.