The first Mennonites came mainly from Swiss and German roots, with many of the important martyrs of the early church coming from the area around Zurich. To escape persecution, many Mennonites fled western Europe for the more accommodating religious climate of the Americas or Catherine the Great’s Russia, giving these two groups distinctly different cultural heritages. When the Russian Mennonites were eventually forced out of Russia in the last half of the 19th Century and the early 20th Century, many migrated to the western states and provinces, where today there is a large Mennonite population. In the second half of the 19th century, the Old Order Movement emerged among Anabaptists of South German and Swiss origin in North America who spoke mostly Pennsylvania German. Most "Old Order" Mennonites emerged through divisions from the main body of Mennonites between 1872 and 1901 in four regions of North America. Indiana in 1872, Ontario in 1889, Pennsylvania in 1893 and Virginia in 1901. Many government and religious leaders, both Protestant and Roman Catholic, considered voluntary church membership to be dangerous—the concern of some deepened by reports of the Münster Rebellion, led by a violent sect of Anabaptists.

They joined forces to fight the movement, using methods such as banishment, torture, burning, drowning or beheading. Despite strong repressive efforts of the state churches, the movement spread slowly around western Europe, primarily along the Rhine[citation needed]. Officials killed many of the earliest Anabaptist leaders in an attempt to purge Europe of the new sect. By 1530, most of the founding leaders had been killed for refusing to renounce their beliefs. Many believed that God did not condone killing or the use of force for any reason and were, therefore, unwilling to fight for their lives. In the early days of the Anabaptist movement, Menno Simons, a Catholic priest in the Low Countries, heard of the movement and started to rethink his Catholic faith. He questioned the doctrine of transubstantiation but was reluctant to leave the Roman Catholic Church. His brother, a member of an Anabaptist group, was killed when he and his companions were attacked and refused to defend themselves.

In 1536, at the age of 40, Simons left the Roman Catholic Church. He soon became a leader within the Anabaptist movement and was wanted by authorities for the rest of his life. His name became associated with scattered groups of nonviolent Anabaptists whom he helped to organize and consolidate. During the 16th century, the Mennonites and other Anabaptists were relentlessly persecuted. In 1693, Jakob Ammann led an effort to reform the Mennonite church in Switzerland and South Germany to include shunning, to hold communion more often, and other differences. Political rulers often admitted the Menists or Mennonites into their states because they were honest, hardworking and peaceful. While Mennonites in Colonial America were enjoying considerable religious freedom, their counterparts in Europe continued to struggle with persecution and temporary refuge under certain ruling monarchs. The Mennonite World Conference was founded at the first conference in Basel, Switzerland, in 1925 to celebrate the 400th anniversary of Anabaptism.