Acute-phase glycoprotein 1H-NMR spectroscopy profiles serve as surrogate markers of chronic inflammation in metabolic disorders such as obesity, diabetes and polycystic ovary syndrome (PCOS). The latter is associated with increased height-to-width (H/W) ratios of GlycA and GlycB after fasting, but not to glycoprotein areas, regardless of obesity. We studied the responses to separate glucose, lipid and protein oral challenges of five glycoprotein variables (GlycA, GlycB, and GlycF areas and the GlycA and GlycB H/W ratios) in 17 women with PCOS, 17 control women, and 19 healthy men. Glucose and protein ingestion resulted into decreases in all glycoprotein variables, whereas lipid ingestion increased GlycA, GlycF and induced minimal changes in GlycB and GlycB H/W. We found no effects of obesity or group of subjects on postprandial glycoprotein variables regardless of the macronutrient being ingested. However, a statistically significant interaction indicated that obesity blunted the decrease in some of these variables in control women and men, whereas obese women with PCOS showed larger changes when compared with their non-obese counterparts. In conclusion, acute-phase glycoprotein profiles indicate an anti-inflammatory response during postprandial phase that is less pronounced after lipid ingestion, and is counteracted by the chronic inflammatory background associated with obesity and PCOS.