According to the World Health Organization, the cutoff hemoglobin (Hb) value for defining anemia is 11 g/dL in preschool-aged children, and Hb measurements should be corrected above an altitude of 1000 meters. This study sought to determine the altitude at which the Hb value increases compared with that at sea level, Hb changes with age and region in Peru, the prevalence of anemia according to three different models used to correct Hb for altitude, and the association of the Hb value with stunting. Two individual-based Peruvian national databases were analyzed. Hb increased from an altitude of 375 meters. Hb concentration was lower at younger ages and higher at older ages. The increase in Hb with increasing altitude was lower in southern Peru. Implementing the different models for Hb measurement correction resulted in a higher and lower prevalence of anemia at altitudes >2500 and <2500 m, respectively, using the CDC adjustment. In children aged 6–23 months, the rate of stunting was lower in those with an Hb level of 10–12 g/dL (including mild anemia). In conclusion, the adjustment of Hb values for altitude should be considered before 1000 m and reference ranges should be adjusted to smaller groups of children instead of the same reference range for children aged 6–59 months.