The small punch test (SPT) is widely used to characterize the ductility and fracture resistance in metals and polymers when only a small volume of material is available. Although the small punch test has been used to characterize biomaterials such as UHMWPE and PMMA, little is known about the application of the small punch test to polyetheretherketone (PEEK). The study was designed to validate the use of SPT with PEEK and its composites and to understand if it could detect differences due to crystallinity level. Unfilled and Radiopaque (RO) PEEK were machined into miniature disks and annealed to 3 crystallinity levels (low, medium, and high). Next, specimens were subjected to bending by indentation with a hemispherical head at a constant rate of 0.5 mm/min to failure while load and displacement were recorded. The SPT was found to reproducibly characterize the mechanical behavior of unfilled and RO PEEK biomaterials. Overall, the differences between filled and unfilled PEEK grades were larger than differences due to annealing. We observed a small influence of crystallinity level on the mechanical behavior of the unfilled material, especially in regards to peak load. Both materials exhibited two distinct fracture patterns, however the variability in fracture behavior appeared to be greater for the RO material. The results suggest that the SPT may be a test method for standardized testing of PEEK biomaterials.