The Sca-1 surface glycoprotein is used routinely as a marker for haematopoietic stem cell enrichment. Two allelic genes, Ly-6A and Ly-6E, encode this marker and appear to be differentially regulated in haematopoietic cells and haematopoietic stem cells. The Sca-1 protein has been shown to be expressed at a greater frequency in these cells from Ly-6A strains of mice. To study the specific expression pattern and haematopoietic regulation of the Ly-6A gene, we constructed a 14 kb cassette from a genomic Ly-6A fragment, inserted a lacZ reporter gene and created transgenic mice. We found that the Ly-6A lacZ transgene was expressed in the haematopoietic tissues and predominantly in the T-lymphoid lineage. Some expression was also found in the B-lymphoid and myeloid lineages. We demonstrated functional haematopoietic stem cell enrichment by sorting for beta-galactosidase-expressing cells from the bone marrow. In addition, we found an interesting embryonic expression pattern in the AGM region, the site of the first haematopoietic stem cell generation. Surprisingly, when compared with data from Ly-6E lacZ transgenic mice, our results suggest that the Ly-6A cassette does not improve lacZ marker gene expression in haematopoietic cells.