Left to right: syringe with case, medical scale, microscope, amputation tourniquet, apothecary box, scalpels, and weights for medical scale.

This section mainly includes surgical instruments, microscopes and other scientific instruments. But in addition, it also contains various types of medical apparatus, uniforms, trophies, ceremonial pieces, and other three-dimensional objects. Many of the items were owned by Jefferson faculty or alumni including bone instruments, a lithotomy knife, and amputation instruments of Samuel D. Gross; an almost complete set of surgical instruments for William W. Keen; and instruments of John Chalmers Da Costa.