Allouez celebrated Mass with a Native American tribe near present-day Oconto, Wisconsin in December 1669, the feast of St. Francis Xavier.

The missionaries worked with the Fox, Sauk, and Winnebago tribes, protected by Fort Francis near Green Bay.

[1] When the British took control of New France in 1763 after the French and Indian Wars, the bishops in Quebec continued to have jurisdiction in the region.

In 1837, the missionary Reverend Florimund J. Bonduel traveled from Green Bay to visit the French fur trader Solomon Juneau in Milwaukee.

The pope named Reverend Michael Heiss of the Diocese of Louisville as the first bishop of La Crosse.

[14] Also in 1971, Heisse invited the Franciscan Sisters of Perpetual Adoration to move their order from Jefferson, Wisconsin, to La Crosse, where they build the St. Rose of Viterbo Convent.

[16] Heiss was succeeded by Reverend Kilian Flasch of the Archdiocese of Milwaukee, appointed by Leo XIII in 1881.

[18] In 1890, the Franciscan Sisters founded the St. Rose Normal School in La Crosse to prepare nuns to serve as teachers.

[20] To replace Flasch, Leo XIII appointed Monsignor James Schwebach, the vicar general of the diocese, in 1892 as the third bishop of La Crosse.

In 1945, Pope Pius XII named Monsignor John Treacy from the Diocese of Cleveland as coadjutor bishop to assist McGavick.

[32] He established a diocesan commission on Christian renewal in 1965, and the first lay ministry training program in the United States in 1975.

He was instrumental in the founding of the Bethany-St. Joseph Care Center for the elderly in La Crosse, a joint venture by the diocese and the Lutheran Church.

[36] Some critics said that construction of the $25 million Shrine of Our Lady of Guadalupe was wasteful of money that should have gone to the poor[citation needed].

Another controversy was the diocese's withdrawal from Church World Service's annual Crop Walk because some of the money raised was being used to purchase condoms in developing countries.

[38] After two years in La Crosse, John Paul II named Burke as archbishop in 2006 of the Archdiocese of St. Louis.

The pope replaced Burke in La Crosse with Auxiliary Bishop Jerome Listecki of the Archdiocese of Chicago.

[39] At La Crosse, he initiated a $50 million fundraising campaign, a planning process to restructure ministry and parishes in the diocese.

[45] As of 2021, the Diocese of La Crosse had 144 diocesan priests, 61 permanent deacons and 197 nuns serving 159 parishes.

[12] The diocese hosts the following religious orders: Reverend Bruce Ball was charged in Jackson County in June 1992 of causing a child to expose a sex organ.

In July 1992, as part of a plea bargain, the Jackson charges were dropped and Ball pleaded guilty to sexual contact with a client.

[48] In January 2002, Reverend Timothy E. Svea from the Institute of Christ the King Sovereign in Wausau was charged with false imprisonment and exposing a child to harmful material.

[50] In May 2019, Monsignor Bernard McGarty was charged with fourth degree sexual assault for allegedly groping a woman outside the La Crosse Public Library.

In December 2021, Richmond pleaded no contest to fourth degree sexual assault, a misdemeanor, and was sentenced to one year of probation.

[56] Viterbo University – La Crosse The diocese operates 74 elementary schools with an approximate enrollment of 8,717 students.