The primary objective of this investigation was to determine whether circadian clock genes were differentially expressed within or among bovine hypothalamic paraventricular nucleus (PVN), anterior pituitary gland (AP), adrenocortical (AC) and adrenomedullary (AM) tissues. The PVN, AP, AC, and AM were isolated from 5-yr-old Brahman cows (n = 8) harvested humanely at an abattoir between 0800-1100 h. Expression of target genes in each sample was evaluated via RNA-sequencing analyses. Gene counts were normalized using the trimmed mean of M values (TMM) method in the edgeR Package from Bioconductor, R. The normalized gene counts of genes important for circadian rhythm were statistically analyzed using the GLM Procedure of SAS. The genes analyzed were circadian locomotor output cycles protein kaput (CLOCK), cryptochrome circadian regulator 1 and 2 (CRY1 and CRY2), aryl hydrocarbon receptor nuclear translocator like (ARNTL), period circadian regulator 1 and 2 (PER1 and PER2), neuronal PAS domain protein 2 (NPAS2), and nuclear receptor subfamily 1 group D member 1 (NR1D1). Overall, relative expression profiles of clock genes differed (P > 0.01) within each tissue with PER1 having greater expression in all tissues (P > 0.01). Within the PVN expression of CLOCK, CRY1, ARNTL, and PER2 was less than that of CRY2, NPAS2, and NR1D1 (P > 0.01). In the AP, with the exception of PER1, no other clock gene differed in degree of expression. In the AC, expression of CLOCK and NPAS2 was greater than CRY1, ARNTL, PER2, and NR1D1 (P > 0.05), whereas CRY2 expression exceeded only CRY1 (P > 0.05). Within the AM, CLOCK and CRY2 expression was greater than CRY1 and ARNTL (P > 0.05). Overall, clock gene expression among tissues differed (P > 0.01) for each individual clock gene. The AC and AM had similar clock gene expression, except expression of CRY2 and PER2 was greater in AM (P > 0.05). The AC and AM had greater expression of CLOCK than the PVN and AP (P > 0.01), with PVN having greater expression than AP (P > 0.01). The AP had greater expression of NPAS2, followed by PVN, with the least expression in the AC and AM (P > 0.01). Both PVN and AP had greater CRY1 and NR1D1 expression than AC or AM (P > 0.01). The AP had greater PER1 expression than PVN, AC, and AM (P > 0.01), whereas PVN, AC, and AM had greater ARNTL expression than AP (P > 0.05). Both AP and AM had greater expression of PER2 than PVN or AC (P > 0.01). The PVN had greater expression of CRY2 than the AP, AC, and AM (P > 0.01). These results indicated that within each tissue the various clock genes were expressed in different quantities. Also, the clock genes were expressed differentially among the tissues of the bovine neuroendocrine adrenal system. Temporal relationships of these genes with the primary endocrine products of these tissues should be investigated to define the roles of peripheral clock genes in regulation of metabolism and health.