Liver receptor homologue 1 (LRH-1) plays important roles in many physiological processes and embryogenesis. However, little is known about the developmental regulation of lrh-1 expression. We identified a novel transcript of mouse lrh-1 (mlrh-1v2) from embryonic stem (ES) cells. mlrh-1v2 is expressed throughout embryogenesis and in several adult tissues, while the known transcript (mlrh-1v1) appears later during embryogenesis. mlrh-1v2 expression is directed by a new promoter which displays a strong activity in ES cells. The generation of the new transcript is conserved in rats. The identification of novel mlrh-1 variant and promoter is critical for elucidating LRH-1 functions in development and adult tissues.