Updated project metadata. Understanding altered expression of proteins and transcripts associated with Toxoplasma gondii infection in cats may improve our understanding of how this parasite manipulates the molecular microenvironment of the definitive host. We performed proteomics analysis of six organs (brain, heart, spleen, liver, lung and small intestine) in cats acutely infected with T. gondii. A total of 32,657 proteins were identified among the six examined organs, including 2,556 differentially expressed proteins (DEPs), of which 1,325 DEPs were up-regulated and 1,231 DEPs were down-regulated. The brain, liver, lung, spleen, heart and small intestine exhibited 125 DEPs, 463 DEPs, 255 DEPs, 283 DEPs, 855 DEPs and 675 DEPs, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed on all proteins and DEPs in all organs, showed that many proteins were enriched in binding, cell part, cell growth and death, signal transduction, translation, sorting and degradation and immune system. Correlation between proteins and transcripts with differential expression patterns were detected in the heart (n = 9), liver (n = 19), lung (n = 9), small intestine (n = 17), and spleen (n = 3). These DEPs were mainly involved in immune response, tryptophan catabolism, and extracellular matrix remodeling. Future investigations are needed to identify the pathophysiological mechanisms underlying the reported associations between the identified proteins and transcripts and T. gondii infection.