Usually 2 or more PI's are used together mostly because it increases drug levels of the PI's. There are many combinations that are used, but the main 2 are saquinavir and ritonavir. As well all potent liver clearing drugs, patients should be monitored for hepatoxic side effects. These combination therapies are also used for aggressive treatment of hepatitis B and C to place back into remission. Insulin resistance, lipodystrophy and hyperlipidemia are the most common long term side effects to the use of PI's.
Kidney stones are also very common, but can be prevented with aggressive hydration.
Generally Recommended Regimens - 2 drugs from a single class of anitretrovirals can be used as the sole regimen. But most experts recommend using 3 or more drugs in combination and using agents from 2 or more classes. And of course there are the unknown side effects when one begins the different combination therapies. Essentially, between the close monitoring relationship of the physician and patient, these drug therapies must be closely monitored to tailor to each patients needs as they arise. Ideally this is the best case scenario, however having a back up drug regimen when developing others is considered the norm should side effects or lifestyle changes or even resistance occurs.