The aim of this study was to compare total outpatient expenditures on hemodialysis and peritoneal dialysis from 2000 to 2004 in patients that began dialysis in 2000 under the Unified National Health System (SUS). A historical cohort was developed, consisting of patients that began dialysis in 2000, identified by probabilistic matching in the database of Authorizations for High-Complexity/High-Cost Procedures (APAC). A multiple linear regression model was used, including individual and clinical attributes and health services supply variables. The cohort included 10,899 patients, 88.5% of whom began hemodialysis and 11.5% peritoneal dialysis. The dialysis modality explains 12% of the variance in expenditures, and patients in peritoneal dialysis showed 20% higher mean annual expenditure. The differences in expenditures are explained according to the State of Brazil and health services supply level. Individual risk variables did not alter the model's explanatory power, while age and diabetes mellitus were significant. The study showed the importance of the National Health System's payment mechanism for explaining differences in expenditures on dialysis treatment in Brazil.