Behavioral and physiological processes have an innate 24-h cycle driven by the circadian master clock, which uses clock genes to generate rhythmicity and distribute temporal signals. Elucidating the blood gene expression in relation to the better known circadian rhythms in horses may contribute to improve the knowledge on the peripheral circadian rhythm control in this species. To do that, seven clinically healthy Italian saddle female horses were housed in individual boxes under natural photoperiod and environmental conditions. In each horse, locomotor activity was recorded continuously; blood samples and rectal temperature were recorded every 4 hours over a 48-hour period. To investigate the peripheral clock in horses, quantitative real-time RT polymerase chain reaction assays were designed to detected clock gene levels (Per 1, Per 2, and Cry 1) from blood samples. Blood cortisol serum level was also measured. Our results showed a daily expression of Per 1, Per 2, and Cry 1 in peripheral blood, associated with the daily rhythm of locomotor activity, rectal temperature and cortisol. In particular, a similar acrophase was observed for locomotor activity and Per 1; and for rectal temperature and Per 2. Rectal temperature and Per 2 also showed the same percentage of robustness of rhythm. We suggest the existence of a linkage between the peripheral clock genes Per 1 and Per 2 with locomotor activity and rectal temperature, although more studies are necessary to establish the exact mechanism of the peripheral clock.