Nidogen, a multifunctional glycoprotein, is an integral part of all basement membranes. In this study, human nidogen cDNAs were isolated and characterized from human placental and skin fibroblast cDNA libraries by hybridization with a mouse nidogen cDNA probe. Six overlapping clones covering 4.9 kb were characterized. The composite cDNA contained a 3,741-nucleotide open reading frame which coded for a 1,247-amino-acid peptide that included a hydrophobic signal sequence. The deduced amino acid sequence contains seven epidermal growth factor-like cysteine-rich repeats, one possible tyrosine O-sulfation site, and a possible N-glycosylation site. The tripeptide sequence -Arg-Gly-Asp- (RGD), a potential cell attachment site, was also present. Human and mouse nidogen sequences were 84% homologous at the nucleotide level and 85% homologous at the deduced amino acid level. Southern blotting of human leukocyte DNA from 23 individuals indicated that nidogen probably is a single-copy gene and shows multiple restriction fragment length polymorphisms when cleaved with Eco RI, Pvu II, Taq I, and Msp I. In particular, digestions with Pvu II revealed polymorphism in four discrete DNA fragments, which could be discriminated by hybridizations with nidogen subclones. One of the polymorphisms revealed an allelic frequency of 0.52/0.48. Thus, human nidogen gene displays RFLPs which provide analytical tools to establish genetic linkage between the nidogen gene and a clinical phenotype.