Nonpoint phosphorus (P) pollution from animal manure is becoming a serious global problem. The current solution for the swine industry includes the enzyme phytase as a component in oil meal and cereal grain-based swine diets. A long-term approach is the production of transgenic phytase pigs that express phytase in the salivary glands and secrete it in the saliva. This study provides a detailed comparison of chemical structures of manure from conventional pigs and transgenic pigs that express phytase under growing and finishing phases using new solid-state NMR techniques. Spectral editing techniques and quantitative NMR techniques were used to identify and quantify specific functional groups. Two-dimensional (1)H- (13)C heteronuclear correlation NMR was used to detect their connectivity. Manure from conventional and transgenic pigs had similar peptide, carbohydrate, and fatty acid components, while those from transgenic pigs contained more carbohydrates and fewer nonpolar alkyls. There was no consistent effect from diets with or without supplemental phosphate or growth stages.