This paper reports a case study of 43 fetuses and perinates from four mass graves and two double burials from the cemetery of St. Jacob in Tartu (SE Estonia). The burials were dated to the 13th–15th centuries AD and located outside the cemetery walls, and likely can be linked to historically recorded episodes of famine and epidemic in medieval Livonia. All individuals belonged to the fetal and perinatal age categories, meaning they were either aborted or died around the time of birth. Ten perinates of these 43 individuals displayed skeletal evidence for systemic metabolic disease. The results of the bioarchaeological investigation provide insights into the effects upheavals of the time had on the weakest members of the society, especially the vulnerability of pregnant and lactating mothers to undernutrition and infections, and shed light on how the prematurely deceased were treated in this urban community. This may potentially explain the burial location. This work is the first detailed paleopathological study of non‐adults in medieval Estonia and the Baltic region, opening the way for further research on similar material in this geographical area.