This review covers our recent advantages in studying the ontogenetic aspects of physiological mechanisms underlying regulation of rhythmic behavior. We have revealed that excitation patterns that emerged at early stages of phylogenetic development of life forms contribute greatly to the rhythmic activity of living vertebrates and invertebrates. These patterns govern spontaneous excitation, which is easily observed during the early stage of ontogenesis. The intensity and patterns of rhythmic activity are determined by nature and kinetics of certain metabolic reactions. During perinatal and sometimes postnatal periods (as in prematurely born animals), endogenic rhythmicity of developing physiological structures is strongly pronounced due to relatively stable living conditions. This rhythmic behavior is coordinated within an entire organism. Its integration in multiple systems is driven by amplitude and frequency modulation yielding rhythms of various frequency ranges. Indeed, it is the complex and conjoint functioning of physiological systems that maintains homeostasis in developing organisms. We present the results of our authentic research concerning the evolution and ontogeny of regulatory mechanisms of motor, cardiovascular, and respiratory systems. The aspects of intact and disrupted development are considered, involving the changes in dopaminergic, norepinephrinergic, and cholinergic system activation.