In Paraguay the highest rate of deforestation was reached in the 2000s, and in some places protected areas are the only remnant of the original ecosystem structure. Paraguay currently has 57 protected areas amounting to 15.2 per cent of the country under protection. In this paper we assess the effectiveness of the Paraguayan system of protected areas (SINASIP) for reptiles' conservation. We generate a matrix of taxa × areas according to 1,789 records for 182 taxa. Areas with the highest number of documented species were
Reserva Ecológica Banco San Miguel y Bahía de Asunción and Reserva de Recursos Manejados Ñu Guazú.Eleven protected areas showed no records. Some species are widely distributed in the country and present in several protected areas, but in other cases numerous species have never been recorded in the protected areas. Three nationally (Phalotris nigrilatus, Philodryas agassizii, and Rhachidelus brazili) and one globally (Philodryas livida) threatened species are currently without protection in Paraguay, as well as the endemic species Homonota rupicola, Ophiodes luciae, Phalotris normanscotti, and Phalotris nigrilatus. At present 90.1 per cent of the total reptiles are found in at least one protected area in the country. Additionally, we show how sampling effort is biased and concentrated around the capital city; and thus a better systematic sampling of the whole country should be considered. Beyond the legal protection provided by protected areas and the strategies to conserve species and their populations, an analysis of the effectiveness of protected areas should be undertaken to secure conservation in perpetuity.