KIR3DL1 is an inhibitory HLA-B receptor of human NK and T cells that exhibits genetic and phenotypic polymorphism. KIR3DL1* 004, a common allotype, cannot be detected on the surface of PBLs using the KIR3DL1-specific Ab DX9. The nature of this phenotype was investigated through comparison of 3DL1* 004 with 3DL1* 002, an allele giving high DX9 binding to cell surfaces. Analysis of Jurkat T cell transfectants with 3DL1* 004 cDNA showed that 3DL1* 004 is poorly expressed at the cell surface, but detectable intracellularly. Analysis of recombinant mutants made between 3DL1* 004 and 3DL1* 002 showed that polymorphism in Ig domains 0 and 1 (D0 and D1) causes the intracellular retention of 3DL1* 004. Reciprocal point mutations were introduced into 3DL1* 004 and 3DL1* 002 at positions 44 and 86 of the D0 domain, where 3DL1* 004 has unique residues, and at position 182 of the D1 domain, where 3DL1* 004 resembles 3DL1* 005, an allotype giving low DX9-binding phenotype. Leucine 86 in 3DL1* 004 is the principal cause of its intracellular retention, with a secondary and additive contribution from serine 182. By contrast, glycine 44, which is naturally present in 3DL1* 004, slightly increased cell surface expression when introduced into 3DL1* 002. In 3DL1* 004, the presence of leucine at position 86 corrupts the WSXPS motif implicated in proper folding of the KIR D0 Ig-like domain. This study demonstrates how a difference between KIR3DL1 allotypes in the D0 domain profoundly affects cell surface expression and function.