The single nucleotide polymorphism (SNP) rs9264942T/C located 35 kb upstream from the HLA-C gene is associated with the level of HLA-C cell surface expression on T cells in a European American population. The association between HLA-C expression and various disease models, including HIV and Crohn’s disease, suggests increased expression can enhance CTL-mediated immune response. The aim of this study was to determine the relationship between donor rs9264942T/C genotype and quantifiable renal transplant biopsy markers. DNA was isolated from peripheral blood of 79 donors. We created an RFLP typing assay to genotype all donors for rs9264942T/C. We separated our cohort into potential high (CC) intermediate (CT) and low (TT) HLA-C expressers. These data were correlated to patient characteristics including quantifiable immunohistochemistry staining in biopsies for cause. We performed an analysis based on the presence or absence of immunohistochemistry staining for IgM, IgA, IgG, C1q, C3, C4 and C4d in a total of 85 renal transplant biopsies taken based on clinical indications ranging from 7 days to 25 years post transplant. The percentage of CC vs CT vs TT rs9264942 genotypes observed in our population are in Hardy–Weinberg equilibrium and correlate with the Caucasian HAPMAP database, a public resource of genotyped SNP data. The TT genotype, considered to have the lowest HLA-C expression, had decreased IgM, IgA, IgG, C4 and C4d positive staining compared to the CC or TC group. There was an inverse correlation with C3 staining where the TT genotype had the highest percentage. This inverse correlation may suggest that in the complement pathway less C3 is converted to C4 and C4d downstream in the TT (low HLA-C expression) group. The frequency of rs9264942T/C in our population was similar to the HAPMAP Caucasian database and is in Hardy–Weinberg equilibrium, allowing us to define high (CC) and low (TT) HLA-C expressers based on the rs9264942 SNP genotype. With this classification we observed patterns in immunohistochemistry staining of biopsies, which suggest low HLA-C expressers have decreased positive staining for immunoglobulins and downstream complement products C4 and C4d.