Immunoglobulin-like transcript 3 (ILT3) is an inhibitory receptor molecule expressed by dendritic cells, monocytes, and endothelial cells. Upon upregulation of ILT3 expression, antigen presenting cells (APCs) become tolerogenic, triggering the differentiation of antigen-specific CD8(+) and CD4(+) regulatory T cells. To analyze the polymorphism of ILT3, we screened DNA from a panel of 150 healthy subjects for single nucleotide polymorphisms (SNPs) within genomic region encoding the extracellular domain (exons 1-8). Here we report the identification of 15 SNPs, including nine nonsynonymous, three synonymous base-pair substitutions, and three intronic, including one deletion polymorphism within 3.6 kb of the ILT3 genomic region. Analysis of three physically linked SNP in healthy individuals indicates that c.356-41-46del, a 6-base-pair (bp) deletion located in intron 3/4, is predominantly associated with c.678A allele, a nonsynonymous SNP located in exon 5. Linkage studies in five nuclear families showed that these two minor alleles co-segregate. Our results demonstrate that ILT3 is highly polymorphic and may be associated with susceptibility to immune disorders.