Mice express CD46 protein and its approximately 1.5-kb mRNA only in the testicular germ cells, unlike primates and pigs which ubiquitously express CD46 and its approximately 4 kb mRNA. Human CD46 is not well expressed in transgenic mice carrying human CD46 cDNA. To analyze the mechanism of regulation of human CD46 expression in mouse cells, we cloned the long (ubiquitous approximately 4 kb, L-form) and short ( approximately 1.5 kb, S-form) forms of human CD46 cDNA whose size difference is due to a stretch of the 3'-UT. Transfection of either cDNA resulted in marked S-form-dependent protein generation in all mouse cell lines tested. In contrast, there were virtually no differences in protein synthesis between S- and L-form cDNA in the simian and swine cell lines. Quantitative mRNA analyses and luciferase reporter gene assays suggested that one major cause of this interspecies discrepancy is transcriptional regulation, i. e. selective suppression of the 4-kb mRNA leading to low levels of protein synthesis. Although other mechanisms such as mRNA stability and translational regulation may lead to the low expression levels of L-form-derived CD46 in mice, the silencer activity in the L-form 3'-UT appears to function in human CD46 transcriptional regulation in mice.