Optimal methods for using dried blood spots (DBSs) for population genetics-based studies have not been well established. Using DBS stored for 8 years from 21 pregnant South African women, we evaluated three methods of gDNA extraction with and without whole-genome amplification (WGA) to characterize immune-related genes interleukin-10 (IL-10), killer immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) class I. We found that the QIAamp DNA mini kit yielded the highest gDNA quality (P< 0.05; Wilcoxon signed rank test) with sufficient yield for subsequent analyses. In contrast, we found that WGA was not reliable for sequence-specific primer polymerase chain reaction (SSP-PCR) analysis of KIR2DL1, KIR2DS1, KIR2DL5 and KIR2DL3 or high-resolution HLA genotyping using a sequence-based approach. We speculate that unequal template amplification by WGA underrepresents gene repertoires determined by sequence-based approaches.