Bartholin visited the Italian botanist Pietro Castelli at Messina in 1644. In 1663 Bartholin bought Hagestedgård, which burned down in 1670 including his library, with the loss of many manuscripts. King Christian V of Denmark appointed Bartholin as his physician with a substantial salary and freed the farm from taxation as recompense for the loss. In 1680 Bartholin's health failed, the farm was sold, and he moved back to Copenhagen, where he died. He was buried in Vor Frue Kirke (Church of Our Lady).