After the United States, Spain comes second in the list of countries receiving migrants from Latin America, and, therefore, it is the European country with the highest expected number of infected patients of Chagas disease. We have studied the National Health System's Hospital Discharge Records Database (CMBD) in order to describe the disease evolution from 1997 to 2011 in Spain. We performed a retrospective descriptive study using CMBD information on hospitalizations including Chagas disease. Data was divided in two periods with similar length in time: 1997-2004 and 2005-2011. Hospitalization rates were calculated and clinical characteristics were described. We used multivariable logistic regression to calculate adjusted odds-ratio (aOR) for the association between various conditions and being hospitalized with organ affectation. A total of 1729 hospitalization records were identified. Hospitalization rates for the two periods were 18 and 242.8/100000 population, respectively. The median age was 35 years (range 0-87), 74% were female and the 16-45 age-group was mostly represented (69.8%). Overall, 23.4% hospitalizations included the diagnosis of Chagas disease with organ complications. Being male [aOR: 1.3 (1.00-1.77)], aged 45 and 64 years [aOR: 2.59 (1.42-4.71)], and a median hospitalization cost above 3,065 euro [aOR: 2.03 (3.73-7.86)] were associated with hospitalizations with organ affectation. Since 2005, the number of detected infections increased in Spain. The predominant patients' profile (asymptomatic women at fertile age) and the conditions associated with organ affectation underlines the need for increased efforts towards the early detection of T cruzi.