The aim of this study was to identify genes involved in human placentation. To do this, differential gene expression was assessed in the decidua (placental bed) from pre-eclamptic and normotensive pregnancies using the polymerase chain reaction (PCR)-based subtractive technique of representational difference analysis. A novel aspartyl protease (cathepsin D-like) cDNA sequence was isolated by virtue of its over-expression in the pre-eclamptic decidual sample tested. It was designated DAP-1 (for Decidual Aspartyl Protease 1). Using DAP-1 primer sequences a second cDNA (DAP-2) was subsequently isolated from decidual RNA by reverse transcription (RT)-PCR and found to be identical to DAP-1 apart from 80 additional and consecutive base pairs in the N-terminal coding region. In DAP-2, a stop codon within the unique 80 bp sequence was predicted to terminate translation immediately before the consensus active site residues. While Southern blotting was used to show that there are two loci with homology to DAP-1 in the human genome, it is postulated that alternative pre-mRNA splicing of the 80 bp exon is involved in the regulated expression of active (DAP-1) and inactive (DAP-2) forms of this novel protease; a mechanism similar to that involved in the regulated expression of Caspase-2, a protease involved in apoptosis. In other systems the regulation of alternative splicing is indicated by tissue specificity and developmental stage specificity of the various spliced products. In this context it was demonstrated that whereas DAP-1 was the major transcript expressed in decidua, the pattern was reversed in the adjacent placental tissue. It is proposed that tissue and developmental stage-specific expression of the DAP protease are important for the normal development and function of the uteroplacental tissues and that dysregulation of the control of DAP gene splicing may play a role in abnormal placentation, like that seen in pre-eclampsia.