Cbfa1 (recently renamed as Runx2) is prerequisite for the differentiation of osteoblasts that play a central role in regulation of bone metabolism. Runx transcription factors belong to Drosophila pair rule gene "runt"' family that also play critical roles during the development of hematopoietic tissues or insect bodies. To identify novel sequences related to Runx (Cbfa) genes, we screened a 11 d.p.c (days postcoitum) mouse embryonic cDNA library using a probe corresponding to Runx2 (Cbfa1) runt domain and identified a novel cDNA fragment. This cDNA (521-41) is about 2.4 kb in length and contains a sequence identical to the N-terminal half of mouse Runx1 (Pebp2 alpha B/Cbfa2/ AML1b) and a novel protein coding sequence in the C-terminal region. High expression levels of 521-41 mRNA were observed during the early mouse embryogenesis, In adult mice, 521-41 mRNA was expressed ubiquitously in lumbar vertebrae, brain, kidney, heart, muscle, and ovary. We also found that 521-41 mRNA was constitutively expressed in an osteoblastlike cell line, MC3T3E1. These data indicate that 521-41 gene is a novel splicing variant of mouse Runx1 which is expressed in skeletal tissues and osteoblastlike cells.