A retrospective analysis was conducted of federal fiscal year (FFY) 2007 New York State Medicaid claims and expenditure data to examine variation in expenditures among New York State Medicaid recipients with HIV disease and the extent to which this variation could be attributed to the prevalence of comorbidities and other chronic conditions unrelated to HIV disease. Median expenditures per person for the period for a high-cost group (those for whom expenditures exceeded $100,000 for the period) were over $157,000, with 40% of total expenditures for this group for treatment unrelated to their HIV disease. The prevalence of comorbidities in the high-cost population is very high, the most common being substance abuse and mental illness.