Background: Hypoglycemia and hypocalcemia are common metabolic disorders in high-risk infants that may cause serious complications in case of late diagnosis. Objectives: This study intended to determine the prevalence of hypoglycemia and hypocalcemia among high-risk infants. Methods: A cross-sectional study was conducted on all the infants prone to hypoglycemia and hypocalcemia admitted to the neonatal ward of Fatemieh Hospital in Hamadan from September 2016 to October 2017. If infants' blood glucose was less than 40 mg/dL within the first four hours after birth and less than 45 mg/dL within 4 -24 hours after birth, they were diagnosed with hypoglycemi. If their blood calcium was less than 7 and 8 mg/dL in preterm and full-term infants, respectively, within 12 -24 hours after birth, they were diagnosed with hypocalcemia. Results: A total of 883 infants participated in this study. The prevalence of hypoglycemia and hypocalcemia was 39.1% and 1.8%, respectively. The mean birth weight was 2124.1 ± 272.8 g, and the gestational age was 35 ± 1.88 weeks. Hypoglycemia had a significant relationship with preterm birth (P = 0.002), lower mean birth weight (P = 0.001), and low Apgar score at 1 and 5 minutes after birth (P < 0.05). Hypocalcemia had a significant relationship with small for gestational age (SGA) (P = 0.007), lower mean birth weight (P = 0.025), and low Apgar score at one and five minutes after birth (P < 0.05). Conclusions: It is recommended to measure blood glucose and blood calcium in high-risk infants, including infants of diabetic mothers (IDMs), preterm infants, and infants with lower birth weight (LBW), SGA, and low Apgar score at one and five minutes after birth.