Background and Aim: Acquired Immunodeficiency Syndrome (AIDS) caused by Human Immunodeficiency Virus (HIV), is a chronic and potentially life-threatening disease. Numerous factors affect its development and progression. Therefore, the present study attempted to identify characteristics impacting the prognosis and progression of AIDS using multistate models. Methods & Materials: The present retrospective study consisted of 2185 patients affected with HIV referring to Behavioral Disease Counseling Centers in Tehran City, Iran, from 2004 to 2013. We considered multiple states of AIDS, tuberculosis, and tuberculosis/AIDS in the natural history of the disease (from the onset of HIV disease until death occurred). Then, we applied the multistate models, to examine the effect of contextual demographic and clinical variables on survival time; subsequently, the transition probabilities of HIV. Ethical Considerations: This study was approved by the Research Ethics Committee of Hamadan University of Medical Sciences (Code: IR.UMSHA.REC.1396.117). Results: HIV-Related deaths in individuals with an incarnation history were 2.40 times higher than in those without the prison history. Death risk was also 1.70 and 1.80 times higher in those aged 25-44 and 44 years, respectively, compared to the individuals aged less than 25 years. An inverse relationship was also found between CD4 levels and the risk of death in our participants. Conclusion: Antiretroviral therapy, CD4 count, age, and history of imprisonment were the main factors in the progression of the disease and subsequent death in HIV patients. Thus, preventing the further spread of the disease to the community and controlling the disease in the patients requires targeted educational and therapeutic interventions; accordingly, the community will be familiarized with transmission routes and the preventing principle of disease. Furthermore, we can encourage patients to visit the healthcare centers early.