This review presents data on the circadian system hierarchy and its unique reorganization at the onset of pregnancy, which plays a fundamental role in maintaining maternal homeostasis and creating optimal conditions for the implementation of the genetic program of fetal development. A particular emphasis is made on the protective mechanisms of the circadian rhythm of maternal melatonin, which is the primary messenger of biorhythms. This paper thoroughly discusses the mechanisms and consequences of maternal chronodisruption in pregnant women exposed to adverse environmental conditions (shift work, stress, irregular nutrition, etc.), as well as in those with chronodestruction-related diseases (obesity, diabetes mellitus, etc.). Elucidating the circadian system status in the patients and, in particular, whether they have a daily rhythm of melatonin production will determine a new approach to risk assessment and timely prevention of cardiovascular, metabolic, neuroendocrine and mental disorders in the offspring in later life.