Human immunodeficiency virus type 1 (HIV-1) protease is a major target in the treatment of HIV-1 infection. It is responsible for the proteolytic processing of viral polyproteins gag and gag-pol that leads to the morphological rearrangements in virion particle known as maturation. As this series of cleavage events is essential for the virus infectivity, inhibitors of the protease are very efficient antiviral drugs. However, the risk of viral resistance is an ever-present factor in the antiviral drug therapy and resistance against all current protease inhibitors is observed. With the ability to tolerate a high number of amino acid side chain substitutions while recognizing and cleaving divergent substrate sequences, the HIV-1 protease has shown to be a challenging drug target. In the present PhD project, a selection system based on the regulatory protein AraC from Escherichia coli was applied for studying drug resistance of HIV-1 protease in different molecular contexts. Inhibitor resistant protease variants were selected from mutant protease libraries, the protease either being part of a polyprotein mimic or active as a free dimer. The distribution and frequency of amino acid side chain substitutions in the inhibitor resistant variants was found to be dependent on the molecular context. In addition, the selected inhibitor resistant proteases appeared to have a more lax substrate specificity compared to the wild type protease. In accordance to this observation, protease variants selected for altered substrate specificity, displayed drug resistance. The findings indicate a strong association between HIV protease drug resistance and substrate specificity.