One of eight patients with nonketotic hyperglycinemia resulted by the lesion in glycine decarboxylase showed the deletion of 0.6-kb SacI and 1.5-kb PstI fragments identified by the cDNA for this protein. A genomic clone, lambda HGDG10, encodes a 5' region of this cDNA in an organized structure and can produce these two fragments. The other clone, lambda HGDG8, carries a processed gene. Southern analysis using a limited segment of this cDNA demonstrated that the 1.7-kb and 1.5-kb PstI fragments predicted from its recognition sites in both genomic clones occur actually in the human genome, indicating that at least two copies of glycine decarboxylase cDNA exist in the haploid genome, and the patient has the glycine decarboxylase gene deleted at a 5' region.