In addition to increasing the health risk to the individual patient, late diagnosis of HIV infection affects the costs of the medical care. Comprehensive data on the precise financial burden posed by late presentation are lacking. This retrospective analysis in Austria aimed to compare the marginal costs of initial care after diagnosis in patients presenting with advanced HIV disease vs. non-late presenters. Treatment-naïve late and non-late presenters were matched by age and risk group and were followed up for an average of 15 months. Using a marginal cost approach, the costs of medications, outpatient consultations, diagnostic interventions, and inpatient stays were compared. Cases had significantly higher viral load and lower CD4 cell counts. At first diagnosis, 45.8 % of cases had CDC stage A vs 85.2 % of controls. Late presenters had 70 % more outpatient consultations (p < 0.01) and three-fold higher total marginal costs (<euro> 722,761 vs. 244,976). Cost per patient and month ranged from <euro> 600 to 17,108 for cases and from <euro> 102 to 26,958 for controls. Largest cost difference was noted for antiretroviral (ART) medication (monthly average <euro> 1,089 per case vs. 77 per control), accounting for 42 % of overall costs for cases compared to 10 % of total costs for the controls. Higher costs were also seen for hospitalizations, diagnostics, and non-ART-medication in cases. Late presentation places a significant economic burden on the Austrian healthcare system. Patients and society would benefit from effective screening programs to enable earlier diagnosis with more efficient linkage to care at least in the period immediately following diagnosis.