In Kenya knowledge of the relative severity of threats to protected areas and the vulnerability of these areas to any threats is lacking. Such information is required, however, for assessment of the effectiveness of management of the country's protected areas, and to help identify critical management and policy weaknesses and priorities for improving management and allocating resources. We therefore studied the relative severity of threats to Kenya's 50 protected areas and their relative vulnerability to such threats based on the perceptions of protected area managers. Ten threats were identified by these managers, of which the most severe were illegal bushmeat hunting, poaching of large mammals, human-wildlife conflicts, human encroachment, and loss of migration corridors and dispersal areas. Thirty-two (64%) protected areas were vulnerable to over half of the threats, 54% vulnerable to over six of the threats and 32% vulnerable to over seven of the threats. Protected areas in marine, forested/montane and inland wetland ecosystems were regarded as highly vulnerable to the perceived threats. Protected areas adjacent to urban/industrial and agricultural areas were vulnerable to most of the threats. Our findings demonstrate that protected areas in Kenya are increasingly threatened, that major threats needs to be mitigated, and that prioritization of protected areas for strategic actions is required for effective management.