The validity of infant mortality data is essential in assessing health care quality and in the setting of preventive measures. This study explores different diagnostic procedures used to determine the cause of death across forensic settings and thus the issue of the reduced validity of data. All records from three forensic medical departments that conducted autopsies on children aged 12 months or younger (n = 204) who died during the years 2007–2016 in Moravia were included. Differences in diagnostic procedures were found to be statistically significant. Each department works with a different set of risk factors and places different emphasis on different types of examination. The most significant differences could be observed in sudden infant death syndrome and suffocation diagnosis frequency. The validity of statistical data on the causes of infant mortality is thus significantly reduced. Therefore, the possibilities of public health and social policy interventions toward preventing sudden and unexpected infant death are extraordinarily complicated by this lack of data validity.