Healthcare providers are often faced with the need to make treatment decisions about antiretroviral therapy regimens for patients with HIV infection without definitive information as to the optimal sequencing of drug regimens. In this paper we describe our model developed to simulate the impact of differing drug sequencing strategies used in the treatment of patients with HIV/AIDS. In addition, we present the methods used to estimate the efficacy and duration of antiretroviral therapies to populate the model at baseline. We conducted a hypothetical application of the model using three alternative series of therapies: a series containing no drug therapy, a series starting with a protease inhibitor-containing regimen, and a series starting with a non-nucleoside reverse transcriptase inhibitor-containing regimen. The model described in this article can be used to compare and contrast the relative impact of different treatment guidelines in the absence of necessary clinical data and may serve as a means of evaluation until clinical trials or observational databases provide guidance as to the optimal treatment regimen(s). The model is flexible and permits adaptation to the changing treatment environment in HIV infection.