The aims of the present study were to examine the serum amino acid profiles in obese and non-obese women and investigate the relationships between the serum amino acids and inflammation and oxidative stress in a human case–control study. Serum amino acids, inflammatory biomarkers (C-reactive protein and IL-6) and oxidative biomarkers (superoxide dismutase, malondialdehyde and glutathione peroxidase) were measured and compared in 235 obese women and 217 non-obese controls. The relationships between serum amino acids and inflammatory and oxidative biomarkers were examined using multiple linear regression. Among the amino acids determined, serum histidine, arginine, threonine, glycine, lysine and serine were found to be significantly lower in obese women as compared to non-obese controls (P < 0·001). The difference was the greatest for histidine (P < 0·001). In obese women, both histidine and arginine were negatively associated with inflammation and oxidative stress. In non-obese controls, histidine was negatively associated with oxidative stress. The findings in this study indicate that the metabolism of amino acids is abnormal in obese women in whom histidine and arginine have close relationships with inflammation and oxidative stress.