The distributions of both the organismal and ecological diversity of Peru were evaluated through cartographic analyses in relationship to Peru's national system of protected areas. Also identified and mapped were areas so poorly known that they represent conservation information gaps, areas that cannot currently be evaluated, but which should not be overlooked. These methods revealed that the protected area system in Peru did not adequately protect either organismal or ecological diversity. In the short term, inclusion of unprotected priority areas in the national system is the best way to improve biological conservation. Over long time periods, it is also important to make decisions about the priority of areas that are information gaps. This study provides a useful point of comparison with other countries that are at different stages in the task of assembling biodiversity information. It was clear that i) the identified priority areas were important for national-level planning; ii) the drier and nonforested ecosystems seldom have been included in conservation efforts; iii) because degradation processes will constantly change, the conservation status of a particular area will also change and should not be confounded in the setting of priorities with the value of the biological diversity present; and iv) the identification of information gaps is the most transparent method for keeping decision-makers advised as to the limits of scientific knowledge on the distribution of biological diversity.