An inventory study of amphibians and reptiles from Karst Zone Batur Agung Gunung Kidul, Yogyakarta was carried out for first time. Exploration was conducted in July-August 2007, May-June 2008 and April 2009 at four districts of Patuk, Playen, Ngawen and Gedangsari. The results showed findings of 9 species of amphibians and 22 species of reptiles. Total of those amphibians and reptiles were recorded, the largest species of amphibian was Duttaphrynus melanostictus (Bufonidae) and Fejervarya limnocharis (Dicroglossidae). The largest species of reptile was Hemydactylus frenatus (Gekkonidae), Lygosoma bowringii (Scincidae), Ramphotyphlops braminus (Typhlopidae), Eutropis multifasciata (Scincidae) and Ahaetulla prasina (Colubridae)