Complete diagnostic autopsy (CDA) remains the gold standard and a valuable technique for determining cause of death. It is a source of health statistics that can be used to measure health care services’ quality, unraveling important information on disease processes, particularly in emerging and unknown diseases. It can also be a vital tool for medical education and biomedical research. However, autopsy rates have been declining globally. There is an urgent need to develop and validate alternative methods in different settings to provide reliable information on cause of death. In this study, we aimed to determine cause of death (KazCoDe) in neonates and infants using minimally invasive tissue sampling (MITS), and to compare these results with those of CDA. We conducted MITS and CDA sequentially on 24 deceased children at the Pathological Bureau of the Akimat of the city of Nur-Sultan. Clinical data of the study subjects were extracted from their clinical records. During both procedures, brain, liver and lung tissues were collected for pathological diagnosis. Fifteen (62.5%) and nine (37.5%) were stillbirths and neonates, respectively. Eight (33.3%) were females and 16 (66.7%) were males. MITS diagnosis of cause of death was concordant with CDA diagnosis in 83.3% out of the 24 cases when considering the immediate and underlying causes of death and reviewing all the clinical and laboratory test results as part of the diagnostic evaluation to arrive at a cause of death (ICD-PM). We concluded that MITS is a valuable and reliable method for cause of death diagnosis in stillbirths and neonates, which can contribute vital mortality statistics in children in the absence of CDA.