As outlined in Part 1 of this 2-part review, there are many choices for the initial treatment of HIV infection. The Department of Health and Human Services HIV treatment guidelines include regimens that are "preferred" or "alternative" for initial therapy. In Part 2 of this review, we discuss those regimens that are considered alternatives, as well as emerging combinations that may be considered for inclusion in future treatment guidelines. With any of these treatments, a change in therapy may be required if drug resistance or intolerance occurs. An initial regimen is important because of its immediate effects and potential influence on the utility of subsequent treatment options. HIV clinicians should be aware of the resistance and safety profiles of all of the various regimens they may prescribe as initial therapy and should be ready to employ a strategy for subsequent treatment in the event of virologic failure or the development of drug toxicity. This article builds on Part 1 by suggesting treatment algorithms for those experiencing adverse events or the emergence of drug resistance when using recommended or common alternative and emerging anti-HIV regimens.