An innate 24 h circadian clock drives various behavioral processes via expression of clock genes that regulate circadian rhythmicity and temporal signals. Elucidating the gene expression in goats may contribute to improving the knowledge of the regulation of circadian rhythms in this species. Five nonpregnant and nonlactating Maltese goats with no evidence of disease were kept in an indoor pen under the natural long photoperiod (05:05–20:56 h) and natural environmental temperature (23°C and 60% RH). They were fed an Alfalfa hay and concentrate mixture provided twice a day; water was available ad libitum. Blood samples were collected every 4 h over a 48 h period into PAX gene Blood RNA Tubes and stored at −80°C until processing. Clock genes (Clock; Cry1; Cry2; Per2; Per3) were determined using real-time quantitative polymerase chain reaction. During the experimental period, locomotor activity was monitored by an actigraphy-based data logger that records a digitally integrated measure of motor activity as a means to assess indices of discomfort during study and stability of the circadian rhythm. All of the tested genes showed daily rhythmicity in their expression in whole blood. Differences in their circadian parameters were observed. Mesor and amplitude were statistically different among the tested gene (Mesor: F(4.30) = 205.30; p < .0001; amplitude: F(4.30) = 104.80; p < .0001), with each gene showing its acrophase at a different time of day (F(4.30) = 81.17; p < .0001), and differences were observed between the two days of monitoring (F(1.30) = 10.25; p = .003). The application of two-way analysis of variance (ANOVA) on robustness of rhythm values did not show statistical differences among the tested genes (F(4.30) = 1.83; p = .14) and between the two days of monitoring (F(1.30) = 1.16; p = .28). Locomotor activity data recording were in accordance with the data reported in literature, indicating the absence of discomfort or alteration of circadian rhythms during the experimental period. Our results support the presence of a cyclic transcription of clock genes in whole blood of healthy goats housed under a long light natural photoperiod and natural environmental conditions.