The circadian timing system orchestrates daily rhythms in physiology and behavior via the suprachiasmatic nucleus (SCN), the master brain clock. Because endocrine secretions have far-reaching influence on the brain and periphery, circadian regulation of hormones is essential for normal functioning and disruptions to circadian timing (e.g., irregular sleep patterns, limited exposure to sunlight, jet lag, nighttime light exposure) have detrimental health consequences. Herein, we provide an overview of circadian timing in three major endocrine axes, the hypothalamo-pituitary-gonadal (HPG), hypothalamo-pituitary-adrenal (HPA) and hypothalamo-pituitary-thyroid (HPT) axes, and then consider the negative health consequences of circadian disruptions in each of these systems. For example, disruptions to HPG axis circadian timing lead to a host of negative reproductive outcomes such as irregular menstrual cycles, low sperm density and increased rates of miscarriages and infertility. Dysregulation of HPA axis timing is associated with obesity and metabolic disease, whereas disruptions to the HPT axis are associated with dysregulated metabolic gene rhythms in the heart. Together, this overview underscores the significance of circadian endocrine rhythms in normal health and disease prevention.