Iron deficiency anemia (IDA) is one of the world's most prevalent nutritional deficiencies, particularly among children. The objective of the present study was to determine the prevalence of IDA among school-age children living two mountainous in rural areas in Morocco. Three hundreds eighty six children (6 to 13 years old) from the provinces of Chefchaouen and Azilal, participated in the study. Anthropometric measurements were determined, and blood samples were obtained by venipuncture for determination of hemoglobin (Hb), serum ferritin (SF), and serum transferrin receptor (TfR). Hb values were determined using Coulter Counter; SF and TfR measurements were determined by ELISA. Mean Hb values were higher for Azilal children (140.1g/L) than those of Chefchaouen (125.7g/L) (p < 0.001). There were no significant differences between boys and girls of the same region. Mean SF values were higher for Azilal children (34.3 g/L) than for those of Chefchaouen (20.2 g/L) (p < 0.001). There were no significant differences of TfR values between Azilal children (9.6mg/L) and those of Chefchaouen (8.8 mg/L). Anemia (Hb < 120g/L) prevalence was higher in Chefchaouen (42.3%) than in Azilal(5.0%); with the highest prevalence among boys (45.5%). IDA (SF < 12g/L and/or TfR > 8.5mg/L) was more prevalent in Chefchaouen (25.1%) than in Azilal (4.5%), with a higher prevalence among boys (31.3%). Further studies, including dietary assessment, are necessary to better understand the cause(s) of IDA, and to recommend appropriate intervention strategy(ies) to combat the anemia.