Asolo - Dutchman , who wore the race leader's pink jersey over the first weeks of the Giro d'Italia, pulled out the race during the 11th stage on Wednesday, according to organisers.
Dumoulin, who rides for Giant, had been suffering from pain in his perineum in recent days and had been using an antiobiotic cream.
But the pain became too much for Dumoulin, who pulled out 95 kilometres into the 227 km 11th stage between Modena and Sestola.
Dumoulin, considered among the possible contenders for overall victory in Turin on May 29, won the opening stage time trial of the race to offer a jubilant start to the Netherlands, who hosted the opening three stages of the 99th edition.
In total he wore the pink jersey for six days. Dumoulin, 25, is now set to turn his focus to reaching peak form for the Rio Olympics road race time trial.