Aims To determine the predictive utility of polygenic risk scores of common variants associated with type 2 diabetes derived from the European and Asian ethnicities among a black South African population. Method Our study was a case-control study nested within the Prospective Urban and Rural Epidemiological (PURE) study of 178 male and female cases, matched for age and gender with 178 controls. Four types of genetic risk scores (GRS) were developed from 66 selected SNPs. These comprised of beta cell related variants (GRSb), variants which had significant associations with T2D in our study (GRSn), variants from the trans-ethnic meta-analysis (GRStrans) and all the 66 selected SNPs (GRSt). Results Of the GRS’s, only GRSn was associated with increased risk of T2D as indicated by an OR (95CI) of 1.21 (1.02–1.43) p-value = 0.015. Stratified analysis of age and BMI, indicated the GRSn to be significantly associated with T2D among the non-obese and participants less than 50 years. The area under the ROC of the T2D risk factors only was 0.652 (p value < 0.001) and with the addition of GRSn it was 0.665 (p value < 0.001). Conclusions The GRS of European and Asian derived variants have limited clinical utility in the black South African population. The inclusion of population specific variants in the GRS is pivotal.