Stained glass is a branch of art which in Switzerland has national importance. The city of Basel was not only formerly a flourishing center of display glass, but also still has in situ a considerable amount of religious and secular stained glass from more modern times (ca. 1830–1930). Therefore stained glass is a field of particular interest to the Basel Historical Museum.

The Museum's stained glass can be divided into four main categories:

• ecclesiastical stained glass from the 13th to the 16th century;
• display glass consisting predominantly of secular panels, beginning in the preReformation period, very well represented for the 16th and 17th century, and including examples of the resurgence of the genre in Basel from about 1830;
• the large homogeneous group of 107 newly made armorial panels donated by Basel families on the occasion of the opening of the Museum in 1894;
• and finally a fourth group of 100 specimen panels produced by apprentice glass painters and copies made in the 19th and early 20th century, which were taken over from the former Museum of Applied Arts in 1989.

The secular stained glass, closely connected with the custom prevalent in Switzerland of donating windows and panels, represents the major part of the collection. These small glass pictures were intended to be viewed at close quarters; they were used to furnish castles, town halls, guildhalls, clubhouses and private living rooms, and consequently come in the form of official glass, glass relating to guilds and societies, and glass bearing the coats of arms of the principal families of the city. About 100 items in the collection can be attributed to Basel masters from the period between 1550 and 1650, a flourishing era when 55 glaziers and glass painters can be shown to have been working in the town. Individual items in the collection prove that the genre was at a peak in Basel in the 16th century, influenced by Hans Holbein the Younger, and underwent a remarkable resurgence in the early 19th century in the person of the glass painter Hieronymus Hess. The collection is completed by drawings and designs for windows in the Museum's graphic art department.