Objective: The objective was to determine the characteristics and factors associated with mortality in patients treated for rare diseases (ER) and catastrophic diseases (EC) in a public hospital in northern Peru. Materials and methods: An analytical cross-sectional study. Data are reported of patients treated in a hospital in northern Peru during 2013. Patients and the disease were characterized and statistical data was obtained. Results: Of the 2316 patients, 2135 (92%) had EC and 181 (8%) ER. The most common disease was nonspecific chronic renal failure (43%), but the hereditary factor VIII deficiency generated higher total spending (more than 850 426,35 €) and higher spending per patient (2115,49 €). The multivariate analysis found an association between mortality and gender (female) (p<0,001, RPa: 1,76, 95%CI:1,67 to1,86), age (p<0,001, RPa: 1,02, 95%CI:1,01 to 1,03) and the number of hospitalized days (p<0,001, RPa: 1,08, 95%CI:1,07 to 1,09). Conclusions: There are economic characteristics and factors associated with mortality in patients in our region. Additional research should be conducted to learn more about this group of patients, which are already generally neglected.