Background Immune thrombocytopenia (ITP), autoimmune hemolytic anemia (AIHA) and autoimmune neutropenia (AIN) are disorders characterized by immune-mediated destruction of hematopoietic cell lineages. A link between pediatric immune cytopenias and inborn errors of immunity (IEI) was established in particular in the combined and chronic forms. Objective Identification of predictive factors of IEI in immune cytopenic children is an important objective for a prompt immunological diagnosis and appropriate management. Aim of this study is to detect clinical and laboratory signs of IEI, in particular the latter by an extensive lymphocyte immunophenotyping. Methods We retrospectively collected 47 pediatric patients with at least one hematological disorder among which persistent/chronic ITP, AIHA and AIN, aged 0–18 years at onset of immune cytopenias and/or immune-dysregulation. The cohort was divided into 2 groups (IEI+ and IEI-), based on the presence/absence of underlying IEI diagnosis. IEI+ group, formed by 19/47 individuals, included: Common variable immune deficiency (9/19), Autoimmune lymphoproliferative syndrome (4/19), DiGeorge syndrome (1/19) and unclassified IEI (5/19). Results IEI prevalence among patients with ITP, AIHA, AIN and Evans Syndrome was respectively of 42%, 64%, 36% and 62%. In IEI+ the extended lymphocyte immunophenotyping identified the presence of statistically significant (p-value<0.05) specific characteristics, namely T/B lymphopenia, decrease in naїve T-cells%, switched memory B-cells%, plasmablasts% and/or immunoglobulins, increase in effector/central memory T-cells% and CD21low B-cells%. Conclusion A wide focused clinical/immunophenotypical characterization of pediatric patients with immune cytopenia can highlight specific signs of IEI, potentially helpful in the diagnostic and clinical management, identifying children worthy of IEI-related molecular analysis.