A nonradioisotopic method has been developed for the determination of all-trans-farnesyl pyrophosphate (FPP), the common intermediate at the branch point of the biosynthesis of cholesterol and nonsterol end products, in dog and human plasma. FPP was cleaved to the parent alcohol, farnesol, by the direct addition of alkaline phosphatase to plasma. Farnesol extracted from plasma was converted into a fluorescent derivative with 9-anthroylcyanide. After the excess reagent was removed using an NH2-bonded phase cartridge, the derivative was separated by a column-switching high-performance liquid chromatographic system, followed by fluorescence detection. A linear response was obtained over the range of 2-18 ng/ml, when FPP was added to dog plasma in which the endogenous FPP concentrations had been lowered to undetectable levels by treatment with an HMG-CoA reductase inhibitor. The endogenous plasma FPP levels in the morning in dog and human detected for the first time by our method were 5.2 and 6.6 ng/ml, respectively. The method was utilized to examine the circadian rhythm of FPP in dog plasma, and different rhythms were observed between feeding and fasting dogs.