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Diarrhea and respiratory diseases are the leading causes of morbidity and mortality among <5-year-olds worldwide, but systematic data are not available from Mauritania. We conducted a hospital-based retrospective study. Data on admissions to Mauritania’s National Referral Hospital (the main pediatric referral center in the country), due to diarrhea and respiratory diseases, during 2011–2014, were analyzed. A total of 3695 children <5 years were hospitalized during this period; 665 (18.0%) due to respiratory diseases, and 829 (22.4%) due to diarrhea. Case fatality rates in the respiratory diseases and diarrhea groups were 18.0% (120/665) and 14.1% (117/829), respectively. The highest frequency of deaths due to diarrhea occurred in the age group 2–5 years (16/76; 21.0%), and due to respiratory diseases in the age group 6–12 months (32/141; 22.6%). We conclude that case fatality rates caused by respiratory diseases and diarrhea are extremely high in children hospitalized at the National Referral Hospital. These data call for intensified efforts to reduce deaths among hospitalized Mauritanian children, and also for integrated control measures to prevent and reduce the burden of both diseases. Additional studies are needed to show the effectiveness of the introduction of vaccination programs for pneumococcal diseases and rotavirus infection in the child population, which were launched in November 2013 and December 2014, respectively.

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