Disclosed herein are single nucleotide polymorphisms (SNPs) characteristic of functional subgroups of KIR3DL1. Also disclosed herein are methods for classifying KIR3DL1 alleles by using a series of oligonucleotide primers and PCR reaction conditions uniquely designed to identify group-specific SNPs from genomic DNA. The compositions and methods disclosed herein are useful in clinical settings and research laboratories, and enable prospective assessment of prognoses of various diseases and selection of most appropriate donors for HCT.