Objective This study was aimed to characterize the swine leukocyte antigen(SLA) class I genes of GGTA1^-/- Wuzhishan minipigs and compare their similarity to human leukocyte antigen(HLA). It has important implications for understanding the cellular rejection in xenotransplantation. Methods Specimens of ear tissue from six founding GGTA1^-/- Wuzhishan minipigs were collected, and the SLA class I genes (SLA-1, SLA-3, SLA-2) were amplified by RT-PCR. Purified products were cloned into pEASY-T1 vectors and sequenced, followed by BLAST alignment and using bioinformatc analysis to characterize the SLA class I genes and compare with the similarity to HLA.Results A total of six alleles were detected, among them alleles were previously reported (SLA-1*0703,SLA-2*1102, SLA-3*0401, SLA-3*0403), and the other were novel (SLA-1*0401wz01, SLA-2*11wz01). The homology between alleles of SLA class I genes in Wuzhishan minipigs and HLA was from 70.5% to 72.1%. The homology analysis of critical amino acid residues on HLA binding with human CD8⁺ molecules showed that SLA-1*0401wz01, SLA-1*0703, SLA-2*11wz01, SLA-2*1102 and SLA-3*0401 occurred mutant at amino acid positions 225 and 228 (T→S,T→M), whereas the other loci were highly conserved. There was a high homology at amino acid level between SLA-2*11wz01, SLA-2*1102 and HLA class I genes which are NK cell KIRs binding sites. Conclusions The amino acid sequences of SLA class I genes of GGTA1^-/- Wuzhishan minipigs have a high homology to HLA. From the point of view of cell-mediated xenograft rejection, the amino acid sequences of SLA class I genes of GGTA1^-/- Wuzhishan minipigs have a high homology to HLA, therefore, Wzhishan minipigs may become a good potential donor for pig-human xenotransplantation.