The objective of this study was to use non-invasive fecal metabolomics to evaluate the effects of contrasting sanitary conditions and associated subclinical health status of pigs. We analyzed fecal metabolite profiles using nuclear magnetic resonance (1H NMR) from pigs aged 14 and 22 weeks. Pigs kept under low and high sanitary conditions (LSC and HSC, respectively) differed in fecal metabolites related to degradation of dietary starch, metabolism of the intestinal microbiome, and degradation of constituents of animal (host) endogenous origin. The metabolites that differed significantly originated from metabolic processes involved in either maintaining nutrient digestion capacity, including metabolism of purines, energy metabolism, bile acid degradation and recycling, or in immune system metabolism. The results showed that the fecal metabolite profiles reflect sanitary conditions under which the pigs are kept. The fecal metabolic profiles strongly resembled previously published profiles of metabolites found in large intestinal digesta in pigs. Fecal valerate content could potentially be used as a biomarker for the immune status of pigs, and kynurenic acid could be used as a biomarker for the porcine inflammatory status of pigs. The use of such non-invasive fecal biomarkers could provide the basis for targeted dietary interventions to reduce the negative impact of elevated immune status on production performance of pigs.