Differentia! diagnosis of the causes of prolonged cough is difficult because of its multifactorial nature. Diagnostics in case of a cough that persists for more than 4 weeks is based on clinical data, but sometimes it is not enough to establish a diagnosis. This issue led to the development of algorithms based on additional diagnostic criteria evaluated with modern non-invasive functional methods for diagnosing diseases accompanied by a prolonged cough in children.Aim. To determine the differential diagnostic value of the functional parameters of the capillary bed, respiratory tract, and autonomic nervous system in children with diseases accompanied by a prolonged cough (more than 4 weeks).Methods. 238 children aged from 2 to 17 years with prolonged cough were examined in inpatient or outpatient settings and divided into 4 groups: Group 1 (n = 68) - patients with acute or exacerbation of the chronic infectious upper respiratory tract diseases; Group 2 (n = 53) - patients with lower respiratory tract infection; Group 3 (n = 39) - patients with allergic rhinitis; Group 4 (n = 78) - patients with bronchial asthma. All patients underwent standard clinical examination. The diagnostic test also included functional assessment of microcirculation, autonomic nervous system, and respiratory system via computer capillaroscopy of the nail bed, evaluation of heart rate variability, and computer bronchophonography.Results. Patients with allergic diseases of the respiratory tract, especially with asthma, show a change in all parts of the capillary bed and a significant increase in the zone of perivascular edema in combination with parasympathicotonia, in contrast to children with infectious diseases of the respiratory system, who showed a change in microcirculation parameters mainly in the venous capillaries in combination with sympathicotonia. In addition, children with prolonged coughing, regardless of its origin, showed functional changes in the high-frequency acoustic parameters of the respiratory system in the form of an increase in the coefficient of the high-frequency acoustic component of breathing (ф3), which indicates bronchial hyperreactivity.Conclusion. The functional parameters of the microvasculature, autonomic nervous system, and respiratory tract can be used as additional differential diagnostic criteria and included in algorithms for diagnosing respiratory diseases of various origins in childhood, contributing to the early detection of the pathology and timely targeted therapy.