A partial cDNA clone encoding cholesterol 7 alpha-hydroxylase (pHA 7 alpha-3) was isolated from a hamster liver cDNA library using rat P-450 ch7 cDNA (p 7 alpha-11) as a probe. In comparison with the complete base sequence of p 7 alpha-11, pHA 7 alpha-3 lacked about 500 base pairs at the 5' end. Circadian rhythms of mRNA for hamster liver 3-hydroxy-3-methylglutaryl coenzyme A reductase and cholesterol 7 alpha-hydroxylase were investigated with cDNA clones encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase (pRed-227) and pHA 7 alpha-3. Typical circadian rhythms of mRNA for both enzymes and a time lag between the two circadian rhythms were observed. The circadian rhythm of activity for each enzyme corresponded to that of each mRNA.