Amino acid metabolism in pregnancy is an important regulatory mechanism for fetal growth and maturation. We aimed to clarify pregnancy-induced changes in amino acid concentrations in maternal plasma by frequent sampling throughout pregnancy and to test the effects of genomic backgrounds on amino acid concentrations. We recruited 19 pregnant women and collected plasma samples monthly during pregnancy and one month after delivery. Amino acid concentrations during pregnancy were analyzed with linear models that considered both individual differences and gestational age. Maternal genotyping was used to evaluate the effects of single-nucleotide variants on the levels of specific amino acids. Significant increases in the amount of threonine, histidine, glutamic acid, aspartic acid and proline and decreases in tryptophan, arginine, valine, and leucine in plasma concentrations of pregnant women were observed as gestation proceeded. Total amino acid concentrations during pregnancy were decreased relative to post-partum concentrations, whereas the ratio of essential to non-essential amino acids was increased across the sampling period. The effects of alternative alleles for three missense SNVs on the concentrations of glycine, asparagine and proline were confirmed in pregnant women and were consistent with a previous report for a non-pregnant population. Principal component analysis of the relative amino acid profiles indicated that principal component (PC) 1 reflected advancing gestation, whereas PC2 was dominated by the difference between pregnant and non-pregnant states. The change in relative compositions of circulating amino acids was a distinctive marker of pregnancy and genomic background dominantly affected maternal metabolic changes in gestation.