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Sickle cell disease (SCD) is one of the most common monogenic disease worldwide. The incidence of SCD is not strictly gender-related as it is transmitted as an autosomal recessive disorder. In particular, the gender-related differences in pediatric SCD are not well-characterized. To address this matter, we retrospectively analyzed the clinical records of 39 pediatric patients with a diagnosis of SCD (hemoglobin SS genotype) focusing on gender differences analyzing various aspects of the disease and comprising both acute symptoms and late complications. We found various gender-related differences in our pediatric population. In particular, pain crisis frequency per year was significantly increased in the male population with a mean number of crisis per year of 1.6 vs. 0.6 in the female population (p = 0.04). Also, severe complications (both infectious and cardiovascular) were mostly found in the male population. SCD-related late cardiac complications were observed mainly in the male population (p = 0.04). Our data support the hypothesis that gender could play a role in determining the clinical course of SCD, even though further studies are needed to assess the exact weight of its influence over the course of the disease. The higher morbidity in males is a well-known feature of SCD in adults and these findings have been only partially studied in the pediatric population. These differences have, in adults, been attributed to hormonal variations found in the two sexes after puberty. In a pediatric population, other factors must be responsible for these discrepancies. These findings suggest that gender could be a valuable factor in the risk stratification of these patients at diagnosis, and possibly guide therapeutic decisions, with the final aim of personalizing the therapy.