Having risen in rebellion against the tyranny of the Spanish Inquisition, they were anxious to preserve their countrymen (only a minority of whom were Protestants) from being placed under the heel of a religious intolerance as narrow and bigoted as that from which they had escaped.

The "Reformed" congregations on the other hand, led by the preachers, were anxious to summon a National Synod for the purpose of creating a State Church to whose tenets, rigidly defined by the Heidelberg catechism and the Netherland confession, all would be required to conform on pain of being deprived of their rights as citizens.

The Libertines were opposed to such a scheme, as an interference with the rights of each province to regulate its own religious affairs, and as an attempt to assert the supremacy of Church over State.
The struggle between the two parties, which had continued intermittently for a number of years, suddenly became acute through the appointment by Maurice of Jacob Harmensz, better known as Arminius, to the Chair of Theology at Leyden, vacated by the death of Junius in 1602.

The leader of the strict Calvinist school, the learned Franciscus Gomarus, had at the time of the appointment of Arminius already been a professor at Leyden for eight years.

Each teacher gathered round him a following of devoted disciples, and a violent collision was inevitable.