It said the bodies of the three were found in the apartment inside Vatican City after a neighbor reported hearing loud noises coming from the commander's apartment.
Alois Estermann, 44, was appointed to the post earlier in the day by the Roman Catholic pontiff. The post had been vacant for nearly seven months and Estermann had been serving as acting commander.
Estermann was married to the Venezuelan-born Gladys Meza Romero for nearly 15 years. Italian media identified the other man found dead as Cedrich Tornay, 23, a non-commissioned officer with the 100-man Swiss Guards corps.
RAI-TV said investigators found Tornay's pistol in the apartment.
An 18-year Swiss veteran of the force, Estermann was one of the few non-noblemen to head the Swiss Guards. The elite, 100-member corps, whose colorful uniforms were designed by Michelangelo, traditionally is headed by a noble.
The job had been open since the previous commander retired in October. The Vatican did not say why it took so long, but most believe it was because of the position's low pay.
Estermann had been the guards' acting commander and had traveled with John Paul on more than 30 trips abroad. He joined the Swiss Guards after four years as an officer in Switzerland's army.
Estermann was present during the 1981 assassination attempt on the pope in St. Peter's Square. After Turk Mehmet Ali Agca fired shots, Estermann sought to shield the pope, news reports said.
The recruits for the special guard must be Roman Catholic men from Switzerland who have served their military duty. They must be under 30 years old and over 5-foot-8, and willing to learn Italian.
Pope Giulio II, who reportedly was impressed by the bravery of Swiss mercenaries, founded the corps in 1506.
Forty recruits were to be sworn in Wednesday, a day the Vatican marks the death of 147 guards who fell protecting Pope Clement VII in 1527.
©1998 The Associated Press. All Rights Reserved. This material may not be published, broadcast, rewritten, or redistributed