The global protected area estate is the world’s largest ever planned land use. Protected areas are not monolithic and vary in their purpose, designation, management and outcomes. The IUCN protected area category system is a typology based on management objectives. It documents protected area types and is increasingly used in laws, policy and planning. As its role grows, the category system must be reactive to opinions and open to modifications. In response to requests from members IUCN undertook a 4-year consultation and recently published revised guidelines for the categories. These made subtle but important changes to the protected area definition, giving greater emphasis to nature conservation, protection over the long term and management effectiveness. It refined some categories and gave principles for application. Debates during revision were intense and highlighted many of the issues and challenges surrounding protected areas in the early 21st century. There was a consensus on many issues including the suitability of different governance models (such as indigenous and community conserved areas), sacred natural sites, moving the emphasis of Category IV from habitat manipulation towards species and habitat protection, and recognition of legally defined zones within a protected area as different categories. However, there was considerable disagreement about the definition of a protected area, the appropriateness of some categories with extensive human use, the possibility of linking category classification with biodiversity outcomes, and recognition of territories of indigenous peoples. We map these debates and propose actions to resolve these issues: a necessary step if the world’s protected area network is to be representative, secure and well managed.