There are over one million people in the United States living with HIV/AIDS, 20% of whom are undiagnosed, increasing the risk of transmission and the burden on the healthcare system. Those with comorbid diseases may be particularly vulnerable. This paper studies the impact of comorbidities, with a particular focus on mental disorders, on HIV patient outcomes as measured by patient length of stay (LOS) and total charges. Generalized linear models (gamma models) allowing heteroscedasticity are developed to characterize the effects of selected comorbidities on HIV patient outcomes in the adult 2006 National Inpatient Sample. Comorbid HIV patients experience different LOS and total charges. In particular, having mental disorders resulted in a decrease in both LOS (19%) and total charges (15%) for HIV patients. To characterize the role of individual mental disorders, principal component and cluster analyses on ICD-9 codes are used to study the impact of mental disorder, and eight conditions are found to be most strongly associated with HIV. Gamma models with these identified mental disorders as independent variables are then developed. The results have shown different effects on LOS and charges for each condition, and special attention should be given to those mental disorders (e.g., drug dependence) that increased LOS and charges when present.