A majority of congenital heart defects are due to abnormal development of the valves and membranous septa, i.e., connective tissue components of the heart. During development, an interesting feature of cardiac connective tissue is transient expression of collagens typical for cartilage. To better understand the role of these collagens in the heart, we have performed a systematic study on the temporospatial expression of type II and IX collagen isoforms during mouse heart development employing northern hybridization and RNase protection assay. The mRNAs for alpha1(II) and alpha1(IX) collagens were expressed transiently between embryonic days 10.5 and 14.5 in embryonic mouse heart. RNase protection assays revealed that for both transcripts the embryonic ("prechondrogenic") variants of the alternatively spliced mRNA isoforms dominated. Immunohistochemistry demonstrated that type IIA collagen and Sox9, its key transcriptional regulator, were expressed in the epithelial-mesenchymal areas of the developing heart, with partially overlapping patterns particularly in valvular and septal regions. In addition, Sox9 expression was detected widely in the developing heart. These observations support the hypothesis that cartilage collagens, especially the long isoform of type II collagen, participate in the morphogenesis of cardiac valves and septa.