We have tested the 5' flanking region of the apolipoprotein A-I (apo A-I) gene, which controls its expression in hepatic cells, for the ability to bind protein factors from rat and rabbit liver nuclei. We found that nuclear extracts from each species contain proteins which bind to three sites in the region which have been shown to be important for control of apo A-I gene transcription. These results contrast with a previous report [Dai, P. H., Lan, S. S. F., Ding, X. H. & Chao, Y. S. (1990) Eur. J. Biochem. 190, 305-310] that no rabbit liver nuclear protein could be detected which binds to the rat apo A-I upstream region and that this lack of binding could explain the failure of the rabbit liver to express the apo A-I gene. We have also shown that the low levels of apo A-I mRNA in the rabbit liver correlate with decreased transcription. Our data suggest that the lack of apo A-I gene expression in liver is a result of transcriptional control but cannot be due to simple lack of protein binding to this region of DNA.