Objective — to study the trend in the incidence and nosological structure of congenital malformations (CMFs) in the fetuses and babies of the Kyzylorda Region (Aral Sea Region) of the Republic of Kazakhstan in the period 2016—2018. Material and methods. Over 2016—2018, the investigators analyzed 550 childbirth histories, the protocol (records) of autopsy in fetuses and babies who had died at the maternity hospitals and children’s hospitals of the Kyzylorda Region (Aral Sea Region, Kazakhstan). Results. Throughout the follow-up period, the structure of CMFs in the Kyzylorda Region, the Republic of Kazakhstan, was found to have 3 major systemic defects: multiple defects; cardiovascular defects, and central nervous system defects, which can be considered as an indicator for environmental problems in the region. There was a preponderance of hydrocephalus and anencephaly among the CMF of the central nervous system and that of interventricular and interatrial septal defects and combined defects among the cardiovascular CMFs. In the considered period of time, malformations of the urinary system, gastrointestinal tract, and lungs were often observed as part of multiple malformations. In the considered period of time, defects of the urinary system, gastrointestinal tract, and lungs were often observed as part of multiple malformations. The postmortem findings indicated that the conformity of clinical and postmortem CMF diagnoses in the Kyzylorda Region were more than 77%.