When the famous bishop of Lund, Peder Winstrup, died in 1679 he was laid to rest in a family crypt in Lund Cathedral alongside his wife. Following a restoration of the Cathedral in the late 19th century, Peder Winstrup’s coffin was moved to the crypt, as the family grave was dismantled. In 2012, a decision was made to move his remains to a different location presenting scientists with an opportunity to investigate bishop’s mummified remains. Unexpectedly, hidden underneath Winstrup’s body, a small bundle containing mummified remains of a 5–6-month-old foetus was found. This finding prompted questions regarding the possible relation between both individuals with most hypotheses suggesting no relation and an opportunistic character of the placement of the foetus in bishop’s coffin. Here we test the hypotheses using ancient DNA genomics, including mitochondrial DNA and Y chromosome data, as tools for kinship analyses. We identified a second-degree kinship relation, which, in combination with genealogical analysis, suggests a grandparent-grandchild relation, as highly probable affiliation.