Short-chain fatty acids (SCFAs) are not only an important energy source, but they also play a regulatory role in various physiological processes in humans and rodents. Current studies, mostly in humans and rodents, have revealed that SCFAs acted as endogenous ligands for G protein-coupled receptor GPR41 and GPR43. Whether proteins similar to human GPR41 and GPR43 mediate the regulatory effects of SCFAs in swine remains unclear to date. The aims of this study were to determine whether GPR41 and GPR43 genes are expressed in porcine different tissues; and whether the expression of GPR41 and GPR43 is tissue-specific and/or time-associated. The alignment results showed that pig chromosome 6 contained GPR41 and GPR43 genes. Reverse transcription polymerase chain reaction (RT-PCR) indicated that GPR41 and GPR43 were expressed in porcine various tissues. The 2218 bp and 1908 bp nucleotide sequence representing the full-length cDNA sequence of porcine GPR41 and GPR43 was obtained from the ileum and spleen using rapid amplification of cDNA ends (RACE), which were capable of encoding 335 and 329 amino acid sequences, respectively. The structure prediction revealed that porcine GPR41 and GPR43 proteins had seven putative trans-membrane domains. The real-time PCR results indicated that GPR41 and GPR43 were expressed throughout the developmental stages in a tissue-specific and time-associated manner. GPR41 and GPR43 were most highly expressed in the ileum (P<0.01) and the spleen (P<0.01), respectively. Western blot results showed that porcine GPR41 and GPR43 proteins were expressed in a variety of porcine tissues, including the spleen, ileum, colon, and adipose tissue. In situ GPR41 and GPR43 immunoreactivities were observed through immunohistochemistry in the spleen, ileum, colon, and adipose tissue. In conclusion, the pig genome encoded GPR41 and GPR43 genes, and these two genes were detected in a variety of porcine tissues and expressed in tissue-specific and time-associated manner.