Three-dimensional printing, especially fused filament fabrication (FFF), offers great possibilities in (bio-)medical applications, but a major downside is the difficulty in sterilizing the produced parts. This study evaluates the questions of whether autoclaving is a possible solution for FFF-printed parts and if the printer itself could be seen as an inherent sterilization method. In a first step, an investigation was performed on the deformation of cylindrically shaped test parts after running them through the autoclaving process. Furthermore, the inherent sterility possibilities of the printing process itself were evaluated using culture medium sterility tests. It could be shown that, depending on the needed accuracy, parts down to a diameter of 5–10 mm can still be sterilized using autoclaving, while finer parts suffer from major deformations. For these, inherent sterilization of the printer itself is an option. During the printing process, over a certain contact time, heat at a higher level than that used in autoclaving is applied to the printed parts. The contact time, depending on the printing parameters, is calculated using the established formula. The results show that for stronger parts, autoclaving offers a cheap and good option for sterilization after FFF-printing. However, the inherent sterility possibilities of the printer itself can be considered, especially when printing with small layer heights for finer parts.