The present research aims to find the association between neonatal anthropometric parameters and zinc and magnesium concentration in cord blood. The current cross-sectional report is a sub-study from the "PERSIAN Birth Cohort Study" conducted on 112 pairs of mother-neonate referring to the index hospitals for giving birth to their children during 2018-19. Umbilical cord blood was collected at delivery for the measurement of zinc and magnesium. Anthropometric indices were measured in standard protocols. Validated questionnaires were used for maternal diet in different trimesters. Dietary patterns were acquired based on exploratory factor analysis. The birth weight was reversely correlated with zinc concentration (r = -0.249, P-value = 0.008); however, the other anthropometric parameters did not show any association with zinc levels (P-value > 0.05). Similar evaluations for magnesium revealed no association between any of the anthropometric indices and this micronutrient agent (P-value > 0.05). Further evaluations represented insignificant differences in both zinc (P-value = 0.51) and magnesium levels (P-value = 0.49) between those with normal versus low birth weight. There was a negative association between the Western dietary pattern in the first trimester of pregnancy and cord blood zinc concentration (β (SE) = -0.21 (0.10); P = 0.026); while healthy and traditional dietary patterns in second and third trimesters were positively related to cord zinc concentration (all P < 0.05). This research did not document a positive statistical association of cord blood zinc and magnesium with birth weight. The association of maternal Western dietary patterns with lower cord blood zinc levels highlights the importance of healthy nutritional habits in pregnancy.