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Comorbidities are defined as the simultaneous occurrence of two or more diseases within the same individual. Comorbidities can delay a patient's recovery and increase the costs of treatment. Assessing comorbidities can provide local health care policy-makers with evidence of the most common multi-health impairments in children. This could aid in redirecting and integrating care and treatment services by increasing health facilities the awareness and readiness of health facilities. The present analysis aims to determine the frequency and associated factors of comorbidities in children with diarrhea in Mozambique. A cross-sectional hospital-based analysis was conducted between January 2015 and December 2019 in children up to 59 months of age who were admitted with diarrhea in six reference hospitals in Mozambique. These hospitals are distributed across the country's three regions, with at least one hospital in each province from each region. Sociodemographic and clinical data were obtained through semi-structured interviews and by reviewing the child clinical process. Descriptive statistics, and Mann-Whitney-U tests were used. Crude and adjusted logistics regression models were built. P-values < 0.05 were considered statistically significant. Comorbidities were observed in 55.5% of patients (389/701; 95%CI: 51.8-59.1). Wasting was the most common comorbidity (30.2%; 212/701) and pneumonia was the least common (1.7%; 12/701). Children born with a low birth weight were 2.420 times more likely to have comorbidities, adjusted odds ratio: 2.420 (95% CI: 1.339-4374). The median (interquartile range) duration of hospitalization was significantly higher in children with comorbidities than without comorbidities, 5 days (3-7) and 4 days (3-6), respectively (p-value < 0.001). One in every two children with diarrhea in Mozambique has an additional health impairment, and this increases the length of their hospital stay.