Background. Recently, there has been an increase in the prevalence of the autonomic nervous system (ANS) dysfunction and, against this background, motility disorders of the upper digestive tract (UDT), which, in turn, is the basis for the formation of chronic pathology of the digestive organs in children. The purpose was to improve the treatment of children with ANS dysfunction by studying the type of motility disorders of the UDT and prescribing therapy schemes depending on the type of disorders. Materials and methods. The article presents the results of clinical and anamnestic, laboratory, instrumental and psychological research of 109 children aged 6–16 years with autonomic dysfunction. Results. All surveyed children were divided into two representative groups: group I (main one, n = 87) — patients with autonomic dysfunction and impaired motility of the UDT who by type of motor function were divided into two subgroups: IA — with the acceleration of this function (n = 18) and IB — with its slowdown (n = 69); group II (comparison one, n = 22) — children with autonomic dysfunction without motility disorders of the UDT. In order to treat patients in subgroup IA, they, in turn, were divided into two therapeutic subgroups: IA1 — only basic therapy for autonomic dysfunction, and IA2 — in addition to basic therapy for autonomic dysfunction, correction of motility disorders of the UDT was performed. Patients of subgroup IB were also divided into two subgroups: IB1 — only basic therapy for autonomic dysfunction, and IB2 — in addition to basic therapy for autonomic dysfunction, correction of motility disorders of the UDT was conducted. The effectiveness of treatment for autonomic dysfunction syndrome has been proven, taking into account the type of motility disorders of the UDT. Different treatment regimens were proposed for children with ANS dysfunction without disorders and with the presence of motility disorders. The use in the comprehensive treatment of children with autonomic dysfunction syndrome of drugs that affect the motor function of the upper alimentary canal significantly increases its effectiveness during treatment for 30 days (89.0 versus 57.0 % when motor function slows down). Conclusions. The effectiveness of the comprehensive treatment for autonomic dysfunction has been proven, taking into account the type of motility disorders of the UDT. It reliably reduces the risk of recurrence of clinical manifestations of gastrointestinal pathology in children.