Introduction: To study the effect of calcium supplementation in pregnancy on NEONATAL Apgar scores and anthropometric indices.Materials and Methods: This cross sectional study was conducted on 1513 pregnant women attending delivery services in the five hospitals (Shohada, Valieasr, Mariam, Lolagar, Akbarabadi) in Tehran and Imam Khomeini hospital in Noor city in north of Iran. Subjects completed a questionnaire that included demographic characteristics and consumption of supplements during pregnancy, then the anthropometric indices and infant’s Apgar score after five minutes was extracted from the newborns files. Of 1513 pregnant women, 835 (55.2%), consumed at least 500 mg of calcium supplements every other day from the18th week through the end of pregnancy.Results: In 1513 infants born in this study, average weight, height, head circumference and Apgar score after five minutes were: 3305.97±451.29 g, 49.99±2.22 cm, 34.12±1.63 cm, and 8.85±0.61 respectively. To evaluate the effect of calcium supplementation on these indices, first we performed T-Test analysis, which showed that it had no significant impact on any of the indices. To assess the impact of all potentially effective factors on NEONATAL Apgar scores and anthropometric indices, linear logistic regression analysis was used and factors (maternal age (>35 and<18), number of pregnancies, preeclampsia, body mass index (BMI), multivitamin supplements, preterm labor, passive smoking, along with calcium supplementation were included in the model. just for birth weight analysis, history of low birth weight was included in the model. Among all the factors studied, for birth weight: preeclampsia (p-value: 0.004, Beta: -2.89), BMI (p-value: 0.002, Beta: +3.10), preterm labor (p-value: 0.00, Beta: -17.20), for height of infants: preeclampsia (p-value: 0.001, Beta: -3.43), preterm labor (p-value: 0.00, Beta: -15.89), for head circumference in newborns: preeclampsia (p-value: 0.030, Beta: -2.20), multivitamin (p-value: 0.00, Beta: +4.16), passive smoking (p-value: 0.00, Beta: +4.00) and preterm labor (p-value: 0.00, Beta: -16.31), and for 5th minute Apgar scores: maternal age (>35 and<18) number of pregnancies (p-value: 0.02, Beta: +2.22), preeclampsia preterm labor (p-value: 0.00, Beta: -8.10), had statistically significant relations.Conclusion: Overall, the results obtained in this study showed no significant relationship between calcium supplementation in pregnancy and improving NEONATAL Apgar scores or anthropometric indices. But preterm labor and preeclampsia were the most effective factors, influencing these indices.