Currently, the concept of a “three-pronged” regulatory “metasystem”, which includes the immune and neuroendocrine regulation circuits, is well recognized. We are also well aware of the changes in each of the regulatory systems in response to man-made chemical factors. The paper presents the mathematical model of functioning of the immune and neuroendocrine systems on the example of the interaction of these systems in response to the introduction of bacterial pathogen. In addition, the model describes the changes in these systems in terms of exposure to chemical factors, taking into account the degree of producing body functional impairment, for example, disruption of the bone marrow. The described mathematical model of regulatory systems is the “meso” level submodel and it is developed within a multi-level model of the functional disorders’ evolution, in which the individual organism is assumed to consist of a finite number of interconnected organs and systems.