In 1495, Basel was incorporated in the Upper Rhenish Imperial Circle, the bishop sitting on the Bench of the Ecclesiastical Princes.

As a direct consequence of the Swabian War, resolved by the 1499 Treaty of Basel, Basel and the Imperial City of Schaffhausen joined the Swiss Confederation in 1501, as the confederacy's 11th and 12th states, with Appenzell following suit 12 years later to complete the Dreizehn Orte that made up Switzerland until the French Revolutionary Wars.

[2] The reformation was brought to Basel by Johannes Oecolampadius cathedral preacher under von Utenheim and co-editor of Erasmus' first edition of the Greek New Testament.

The first edition of Christianae religionis institutio (Institutes of the Christian Religion – John Calvin's great exposition of Calvinist doctrine) was published at Basel in March 1536.

[4] In 1543, De humani corporis fabrica, the first book on human anatomy, was published and printed in Basel by Andreas Vesalius (1514–1564).

At a meeting in Bad Bubendorf on 18 October 1830, 25 Baselbieter wrote to the "esteemed gentlemen and noblemen in Basel", demanding equal rights between city and countryside and a representation in parliament in proportion to their numbers.

A number of villages, such as Gelterkinden, Reigoldswil, Anwil and Bubendorf remained loyal to Basel, though coming under threat from the rebels.

After this conflict, the highest Swiss authority, the Tagsatzung, was petitioned on 17 August 1833 to separate the canton of Basel; nine days later, the partition into half-cantons, modelled after the precedent of Unterwalden and Appenzell, was effected.