Fluoropyrimidines induce cytotoxicity, in part, by inhibiting the proliferation-coordinated enzyme thymidylate synthase (TS), which is essential for DNA synthesis. Tumor TS levels are clinically predictive of post-surgical tumor recurrence and of response to fluoropyrimidine chemotherapy. Fluoropyrimidine drug toxicity and efficacy each vary reproducibly in humans and animals, depending upon their circadian timing. In vivo, normal tissues and some tumor tissues exhibit circadian coordination of cellular proliferation. We therefore asked whether TS activity is coordinated rhythmically throughout the day in the normal proliferative tissues most damaged by fluoropyrimidine drugs. To assess tissue and time of day TS activity differences, we harvested normal tissues from female mice living on a 12:12 hr light:dark schedule at each of 6 different equispaced times throughout a 24 hr cycle and measured TS catalytic activity. We observed up to 10-fold differences in vivo in TS activity among different normal tissue types, roughly paralleling their proliferative state and relative fluoropyrimidine sensitivity. In normal tissues most damaged by fluoropyrimidines (bone marrow, small intestinal mucosa and oral mucosa/tongue), TS activity varies up to 2-fold throughout each day. In bone marrow, the circadian pattern of TS activity parallels the circadian rhythm in proliferation in this tissue. This circadian organization of TS, one of the primary fluoropyrimidine targets in normal tissues, probably contributes in vivo to the time of day differences in the toxic-therapeutic ratio of circadian-timed fluoropyrimidine drug therapy.