Any pills that you take go through the stomach. Most drugs are absorbed faster if the stomach is empty. For some medications, this is a good thing, but it can also cause more side effects. Some medications need to be taken with food so that they are broken down more slowly or to reduce their side effects. Other medications are taken with fatty foods because they dissolve in fat and are absorbed better.
Stomach acid can also make a difference.
Protease inhibitors and non-nucleoside reverse transcriptase inhibitors are processed by the liver and cause many drug interactions. Everyone taking anti-HIV drugs needs to be very careful about drug interactions. This is not a complete list. Other drugs may also cause interactions. Ask for this information for each drug that you are taking.