We have previously shown that polymorphisms in the promoter of the human platelet-derived growth factor alpha-receptor (PDGFRA) gene can be grouped into five distinct haplotypes, designated H1, H 2 alpha, H 2 beta, H 2 gamma and H 2 delta, and that specific combinations of these promoter haplotypes predispose to neural tube defects (NTDs). These promoter haplotypes differ strongly in their ability to drive reporter gene expression in various human cell lines, with highest activity for H 2 alpha and H 2 beta. Here, we show that the haplotype-linked PDGFRA promoter region extends to 3.6 kb upstream from the transcription start site, and contains a total of ten polymorphic sites. For two of these polymorphic sites, i.e. -909 C/A and +68 GAins/del, we observed differential binding of nuclear proteins from human osteosarcoma (HOS) cells. The protein complex binding specifically to -909 C, which is present in all haplotypes except the low activity haplotype H 2 gamma, contained members of the upstream stimulatory factor (USF) family of transcription factors. Furthermore, we identified a protein complex of 125 kDa which bound specifically to the low activity haplotype H1 at position +68 GAdel and may represent an H1-specific PDGFRA transcriptional repressor. The current identification of cis-acting elements in the PDGFRA promoter and the transcription factors that bind them, provides a new strategy for the identification of genes that are potentially involved in neural tube defects.