OBJECTIVES: Neglected diseases (ND) are a group of illness caused by infectious and parasitic agents endemic in low-income populations. ND control is essential for achieving country development and inequalities reduction. The Brazilian Program for Research and Development in Neglected Diseases (BPRDND) was created by the Brazilian Ministry of Health. Seven priorities were established: dengue, Chagas disease, leishmaniasis, hanseniasis, malaria, schistosomiasis and tuberculosis. This study aims to evaluate hospitalization patterns and costs related to those diseases after BPRDND implementation. METHODS: Analysis of reported ND related hospital admissions was developed according to ICD-10 classification as described in Brazilian Hospital Information System (SIH/SUS) database, from January 2009 to December 2011. Only seven priority diseases were included. Costs represent federal reimbursement values for hospitalizations (medical procedures, exams, drugs and fees) estimated in 2014 Brazilian Real (BRL). RESULTS: From 2009 to 2011, 306,682 hospitalizations due to all selected ND were observed and dengue represented 70.22% of all. Dengue treatment was responsible for 69.58% of ND related procedures. Total cost was 162,458,715BRL in the period with 46.22% and 41.78% due to tuberculosis and dengue, respectively. Over the years, cost distribution was: 16,039,294BRL in 2009, 27,970,785BRL in 2010, and 23,869,733BRL in 2011 for dengue, and 21,791,027BRL in 2009, 23,889,130BRL in 2010 and 29,410,353BRL in 2011 for tuberculosis. Compared to 2009, 2011 showed an increase of 39% and 37% in hospitalizations and associated costs, respectively. In-hospital deaths presented an increase of 9.7%, except for Chagas disease and schistosomiasis, with reduction of 45% and 56%, respectively. Geographic distribution indicated northeast region accounting for 39.47% of hospital admissions, and 35.72% of costs, followed by southeast (23.02% and 29.79%, respectively) and north region (20.02% and 13%, respectively).    CONCLUSIONS: Despite the implementation of PRDND in Brazil, this class of diseases still presents high frequency of hospitalization and costs, specially dengue and tuberculosis.