Just to make one thing clear: caves are not the source of unimaginable diseases, thats a fantasy from horror movies. Right in the contrary: the high humidity condensates on dust and bacteria, they become heavier and fall down to the ground. So the air in cave is extremely clean and free of irritants. The high amount of carbon dioxide has a soothing effect on the respiratory system, which is used for the so-caled speleotherapy.
But obviously there is another side of this. Especially tropic caves may contain pathogens, under certain circumstances a disease finds ideal conditions in a cave.
The most important group of diseases is passed on by the most common cave animals, bats. The dry dropping for dust, which is swirled up by air currents or walking cavers. The pathogen is inhaled and may infect the lungs. Also it should be avoided to touch bats, as they might scratch or bite, which could also transfer pathogens.
The second source of diseases are ticks, during the bite numerous pathogen may be released into the blood stream. Mostly ticks are a problem on the surface, but some are living in caves. And it is common that cavers looking for a cave catch a tick on the way.
The third source of diseases is the water in caves. The first caver of the world, E.A. Martell, learned this when he drank water from a cave river. He became very ill, and after he had recovered he looked for the source of the water. At the upper end of the cave he discovered a dead cow, which was thrown into the cave opening. What you should learn is simple: anything which contaminates the water on the surface will still be there underground. So be extremely carefull in tropic countries, were some diseases you can get from water need only contact to the skin.
The health risks of caves are well known to experienced cavers. We try to make them aware to the average cave tourist, because of the increasing amount of travelers visitng caves in exotic countries. On such visits, most people tend to ignore any negative thought and trust the local guides. There are few cases of diseases, which can be connected with cave visits, but most of them could have been avoided, if the people had been more responsible themselves.