Interaction of slow-wave rhythmic components of cardiac, respiratory and motor activities was analyzed in non-narcotized neonatal (P1) and early postnatal (P16) rat pups under normal conditions and after activation of cholinoreactive structures. A reversible acetylcholinesterase (AChE) inhibitor physostigmine (eserine) and the M-cholinolytic methacin were used in the experiments. It was established that in intact P1 rats intersystemic interactions are mainly realized via oscillations within the near- and multi-minute ranges. Correlative interactions between the rhythms in the decasecond range that were not involved in integrative processes in P1 rats increased significantly at P16. In rat pups of both ages, changes in the intensity and pattern of motor activity (MA) tended to precede the generation of modulatory oscillations of the respiratory and heart rates. AChE inhibition by physostigmine and subsequent activation of cholinoreactive structures evoked a decrease in the level of intersystemic interactions across all ranges of the modulatory rhythms in rats of both ages. The methacin-evoked blockade of peripheral M-cholinoreceptors (M-ChRs) decreased the level of interactions mediated by the near- and multi-minute rhythms at P1 but augmented them at P16. Physostigmine injection at P1 and P16 exerted no significant effect on cardio-somatomotor interactions, with these interactions in P1 rats being maintained by a wider range of the modulatory rhythms. The same situation was also observed during the physostigmine aftereffect period in all interacting systemic pairs. By contrast, after the blockade of peripheral M-ChRs the existing intersystemic interactions were more difficult to be disrupted in P16 rat pups. The activation of cholinoreactive structures, which occurred against the background of M-ChRs blockade, led to disrupt the coordinating interactions in the “MA–respiratory rate” pair. In P1 rats, these functional relationships did not recover, while in P16 rats they were resumed already during the aftereffect period. The power of modulatory rhythms of activity in the systems studied here was not directly related to intersystemic interactions. Changes in intersystemic interactions were due to heterochrony both in the maturation of these functional systems and the involvement of different cholinoreactive structures in the processes of intersystemic regulation.