In total, there are more than 1,100 caves and abysses in the Moravian Karst. They were formed by gradual erosion and corrosion activities of atmospheric water and its subterranean streams in tectonically disturbed and relatively soluble layers of limestones.

The Výpustek Cave system was created in several development phases due to ponor activities of the Křtinský Brook and its tributaries. The extent and the arrangement of underground spaces probably even influenced the underground drainage of the Babická plain.

There are two levels of the Výpustek Cave. From the point of view of development, the older spaces of the upper level of the cave are more colossal and more extensive. The lower level lies 40 m deeper and it is known so far only in several short sections where the underground Křtinský Brook flows. Both cave levels are connected with abysses, some of which are filled up today. After several kilometres of unknown underground, the Křtinský Brook appears again on the surface in the Otevřená skála doline near the road.

A substantial part of spaces of the upper level was filled with clay sediments with high content of phosphates and numerous skeletal remains of Pleistocene vertebrates. Under the earth there are sometimes places with river gravels documenting ancient activities of subterranean streams. Considering the fact that during most of the 20th century the Výpustek Cave was not accessible to speleologists and many entries into the side passages were walled up, the hydrography and paleohydrography of this complicated cave system is not quite understood yet. The spaces of the cave, especially its lower levels, have appeared in many legends since medieval times. There are also reports from the first half of the 20th century of spacious corridors of the lower levels that are not known at the present time.