BACKGROUND: The aim of this study was to investigate the metabolomic changes in the spleens of ducks artificially infected with Clostridium perfringens type A. Twenty-four healthy ducks aged 1 d were used for this purpose. After acclimatization for 37 d, the ducks were divided into 4 treatment groups (n = 6): the control group (normal group), infection Group 1 (66 h), infection Group 2 (90 h) and infection Group 3 (114 h). The ducks in the corresponding infection group were challenged with 8 mL of C. perfringens type A bacterial solution (1 × 10(8) CFU/mL) for 4 days. The experimental ducks were culled at 0 h, 66 h, 90 h and 114 h after infection, and the ducks were sacrificed for spleen sampling at the end of the experiment. Autopsy observations, spleen pathological changes and pathogen nucleic acid detection were also performed. Finally, the changes in the metabolic profile of the spleen were investigated via a metabolomics approach. RESULTS: At necropsy, the pathological changes in C. perfringens type A infection included enlarged, haemorrhagic and mottled spleens. Histopathology examination revealed that the ducks in the infection group had damaged spleen tissue structures, dilated spleen sinuses with congestion and bleeding, an extreme decrease in lymphocytes, and massive inflammatory cell infiltration in the splenic tissue. Spleen lesions were observed and PCR tests were positive in ducks in the infection group, indicating that a model of C. perfringens type A infection was successfully established in this study. Compared with those in the normal group, 14, 15 and 20 differentially abundant metabolites were identified after 66, 90 and 114 h, respectively, of C. perfringens type A infection of duck spleens, mainly including indolin-2-one, 3-methylindole, 4-hydroxy-2-quinolinecarboxylic acid, indole-3-methyl acetate, uric acid, 2'-deoxyinosine, urate, xanthine, 3-succinoylpyridine, nicotinic acid, phenylacetylglycine, histamine and phosphoenolpyruvate. Pathway analysis revealed that these metabolites were mainly involved in tryptophan metabolism, purine metabolism, nicotinate and nicotinamide metabolism, phenylalanine metabolism, histidine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, tyrosine metabolism, arginine and proline metabolism, arachidonic acid metabolism, and caffeine metabolism. CONCLUSIONS: These findings suggest that C. perfringens type A infection causes a duck spleen inflammatory response and immune response in infected ducks through indolin-2-one, 3-methylindole, 4-hydroxy-2-quinolinecarboxylic acid and tryptophan metabolism, purine metabolism, nicotinic acid and nicotinamide metabolism, which provides a basis for understanding the pathogenesis of C. perfringens type A in ducks.