Illegal killings of protected species may significantly affect their population status or lower recovery rates after protection. Poaching is difficult to monitor directly, hence indirect methods are required to document poaching incidences and levels. The use of shotguns inevitably results in wounding some animals that are not killed. Inefficient hunting methods may result in high annual infliction rates in game species. To reduce wounding of game species, an action plan was implemented in Denmark. Using X-ray analysis, we monitor trends in prevalence of embedded shotgun pellets in the legally hunted red fox (Vulpes vulpes) after the implementation of the action plan, and assess poaching levels of two protected species, the otter (Lutra lutra) and the badger (Meles meles) in Denmark. Overall, 13.8% of the red foxes and 6.9% of the otters carried embedded shotgun pellets, while none were recorded in badgers. The prevalence of embedded shotgun pellets in red foxes declined from 24.9% to 8.5% from the late 1990s to the late 2000s, while no change was recorded in otters. Prevalence of embedded shotgun pellets was similar in otters and red foxes collected in the late 2000s. The decline in wounded red foxes suggests that the hunting methods have changed after the action plan was implemented in Denmark. The high proportion of otters carrying embedded shotgun pellets shows that there is a significant poaching of this protected species in Denmark, possibly by hunters and fish farmers that cannot distinguish between otter and non-native American mink (Neovison vison).