Restriction fragment length polymorphism analysis of the human CD46 gene, which encodes a cell surface complement regulatory protein, has been performed using a 1.5-kb cDNA probe containing a complete CD46 coding sequence. The sum of the invariant band sizes indicates that this gene encompasses at least 35-kb genomic DNA. Polymorphisms were detected in normal individuals with both HindIII and EcoRI. Several of the polymorphic bands occurred significantly less frequently in recurrent spontaneous abortion individuals. Northern blot analysis has shown the predominant RNA transcript size to be 4.2 kb in trophoblast-derived cell lines and peripheral blood mononuclear cells, indicating these transcripts may contain an unusually long 3'-untranslated region.