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Introduction A scientifically-based knowledge on the incidence, dynamics of detection and structure of congenital malformations of the musculoskeletal system (CMMS) has both practical and scientific significance. For many years, the Turner Institute has close scientific and practical ties with the state public health institution "Diagnostic Medical and Genetic Center" of St. Petersburg which carries out a regional monitoring of congenital disorders in St.Petersburg. Our objective was to present regional statistical data on the CMMS detection and structure in newborns and children of the first and second years of life, morbidity and disability in children aged 0-17 years in connection with congenital malformations of the musculoskeletal system, to study the proportion of CMMS patients in the orthopedic clinic and their need for surgical, including high-tech, treatment, and dispensary follow-ups in outpatient orthopaedic settings. Material and methods Regional statistics of St. Petersburg on prevalence, dynamics and structure of congenital malformations of the musculoskeletal system in children born in St. Petersburg in 2001–2015 were analyzed. The statistical data on the prevalence of congenital malformations of the musculoskeletal system in children aged 0–17 years in St. Petersburg were studied. Based on the studies conducted at the Turner Institute in 2014–2016, the proportion of patients treated for congenital malformations of the musculoskeletal system was revealed as well as their need for surgical treatment. Peculiarities of dispensary follow-ups of CMMS patients at orthopedic consultations of children's clinics of St. Petersburg were analyzed. Results and discussion The prevalence and structure of congenital malformations of the musculoskeletal system in 783,000 children born in St. Petersburg in the period of 2001–2015 are presented in accordance with blocks Q65–Q79 of ICD-10. Diagnostic results of congenital malformations of the musculoskeletal system in newborns (2.70 ‰) and in children of the same group until they reached three years of age (4.21 ‰) were studied in dynamics. Infacnts and children up to 17 years old with congenital malformations of the musculoskeletal system are under regular supervision of orthopedic surgeons. Disability due to congenital anomalies and malformations takes the third place among all the diseases detected in patients aged 0-17 years, established by pediatric medical and social expert boards of St. Petersburg. At the clinic of the Turner Institute, the proportion of patients with CMMS among all admitted patients was 38.6 %. Among them, 78 % of patients with CMMS received surgical treatment, of which 80 % of operations were performed using high technologies. Conclusions Statistics on congenital malformations of the musculoskeletal system in newborns and children under 3 years old and a high level of their disability shows the need in a specialized care for these children, including high-tech surgical treatment.