Perinatal hypoxia is one of the more common complications of the early adaptation period. This condition is defined as a disorder of tissue oxygenation during labour and is responsible for approximately 23% of neonatal mortality. Perinatal hypoxia can cause injury and failure of many organs, including the brain, heart and kidneys, mainly in the mechanism of the ischaemic-reperfusion injury. Currently, biochemical markers are more frequently incorporated in neonatal diagnostics. Routinely used in adult patients, these organ-specific chemicals enable diagnosis with high sensitivity and specificity. The manuscript presents a review of research on the use of cardiac markers (N-terminal fragment of pro-B-type natriuretic peptide, cardiac troponins I and T, and cardiac creatine kinase isoenzyme) in selected neonatal diseases. Still, no cutoff values have been established for any of the markers described in this paper. Therefore, for routine use of cardiac markers in the neonatal population, further studies are needed to determine the range of cutoff values and factors that may cause their fluctuation.