C. difficile infections have become a major challenge in medical facilities today. The bacterium is capable of spore formation, which even allows survival of antibiotic treatment. Therefore, research on the physiology of C. difficile is important for the development of alternative treatment strategies. In this study, we investigated eight putative flavodoxins of C. difficile 630. Flavodoxins are small electron transfer proteins of specifically low potential. The unusually high number of flavodoxins in C. difficile compared to other bacteria suggests that they are expressed under different conditions. Therefore, we investigated expression along bacterial growth and found high transcription levels during the exponential growth phase, especially for floX. Since flavodoxins in other bacteria are capable of replacing ferredoxins with their [2Fe-2S] clusters under iron deficiency conditions, we also examined flavodoxin expression in C. difficile under low iron and no iron levels.