We have cloned and sequenced the mouse transcript homologous to human polycystic kidney disease 1 (PKD1). The predicted protein is 79% identical to human PKD1 and shows the presence of most of the domains identified in the human sequence. Since the mouse homolog is transcribed from a unique gene and there are no transcribed, closely related copies as has been observed for human PKD1, we have been able to investigate alternative splicing of the transcript. At the junction of exons 12 and 13, several different splicing variants lead to a predicted protein that would be secreted. These forms are predominantly found in newborn brain, while in kidney the transcript homologous to the previously described human RNA predominates.