We have previously described the purification and partial characterization of the rat analogue of the human complement regulatory molecule CD59 [Hughes, Piddlesden, Williams, Harrison and Morgan (1992) Biochem. J. 284, 169-176]. We present here the molecular cloning and full sequence analysis of this molecule. A PCR-based approach utilizing primers designed from the amino-terminal protein sequence was used to isolate a full-length cDNA clone from a rat kidney cDNA library. This clone encoded a 92 bp 5'-flanking sequence, a 66 bp signal peptide and a 315 bp coding region containing putative glycosylation and GPI-anchor signals. The 3' untranslated flanking region was approximately 1.1 kbp long and included the poly-A tail and a CATA repeating sequence. The coding region was 58% identical with the human cDNA at the nucleotide level and 44% identical at the amino acid level. Despite this relatively low overall sequence conservation, several highly conserved stretches were apparent, particularly in the N-terminal portion of the molecule, in the cysteine-rich region immediately preceding the site of glycolipid attachment and in the C-terminal peptide removed during glycolipid attachment. An N-glycosylation site was identified at Asn-16 and a putative glycosylphosphatidylinositol anchor addition site at Asn-79, indicating that the mature processed protein was two residues longer than human CD59. Comparison of the sequences of rat and human CD59, together with consideration of the published three-dimensional structure of human CD59 and functional data, implicates specific regions of the protein in interactions with C-8 and/or C-9.