Plasma filaments have been measured with alkali beam emission spectroscopy in the plasma edge, divertor island, and scrape-off layer of Wendelstein 7-X. Due to the high intensity of a 1–2 kHz plasma mode, a new, correlation based conditional averaging algorithm was used to search for filaments in the signals. With that method, effects of different magnetic configurations and density levels on filament properties are observed. In configurations where the islands are small and do not play an important role for the connection length topology, filaments behave similar to tokamaks. In contrast, in configurations with larger magnetic islands and more complex connection length profiles, filaments behave quite differently, for instance they may or may not appear in the inner side of the divertor island depending on the plasma parameters. Coupling between the filaments and lower frequency events are also showed. The role of filaments in the global and local particle transport is briefly discussed.