Despite its small size Austria is home to about 16,000 caves. The vast majority is epigene in origin and occurs in uplifted karst plateaus. Only about hundred caves of hypogene origin are known, whose features and modes of origin are reviewed in this article. Most currently known hypogene caves cluster along the rim of the southern Vienna Basin. Some of these caves, including Eisensteinhohle, are characterized by a slight thermal anomaly associated with warm springs. A second province with hypogene karst features is also structurally controlled and occurs south of the Salzach fault in the Central Alps, where caves show morphologies, mineralization and geochemical patterns diagnostic of hypogene origin. In the same area lukewarm springs emerge at lower elevations. A third region where hypogene processes resulted in cave development is the area of the Periadriatic Lineament in Carinthia. Caves such as Kozakhohle show Laughohle morphologies and are perched above the valleys, but the presence of CO2-rich springs suggests that speleogenesis may still be ongoing in the subsurface. Only very few hypogene caves are currently known from the Northern Calcareous Alps (NCA). Most of those seem again to be related to upwelling of aggressive waters enriched in CO2, while only one cave in this part of the Eastern Alps shows evidence of sulfuric acid speleogenesis (Kraushohle). Radiometric dates constrain the final stage of the process to between about 160 and 86 ka before present, while the presence of a lukewarm H2S-bearing spring in a gorge below the cave provides evidence of minor water–rock interactions involving dissolved sulfur species still operating today at this site.