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Background Autoimmune manifestations in primary immunodeficiencies (PIDs) are not uncommon, and they are more frequently observed in defects affecting lymphocytes and their regulatory mechanisms. There is a wide variability in prevalence, ranging from immune defects in which autoimmunity defines the syndrome, others with a very high prevalence of autoimmune manifestations, defects with a moderate prevalence, and those in which autoimmunity is rather an exception than the rule. Objective We aimed to determine the prevalence of autoimmunity in children with PIDs from our hospital, to delineate their clinical features. Methods An internal register was consulted to identify autoimmune diseases in our patients with PIDs. Their clinical files were then reviewed for diagnostic workup, age of presentation and outcome. Results We identified a prevalence of 18.8% (47 out of 250 patients, 68.1% male patient), within a period of 40 years (1970–2010), with autoimmune manifestations in the context of PID. Of which most are still alive: 35 (74.5%); lost to follow-up: 3 (6.4%), Dead: 9. Known or probable consanguinity was reported in 25.4%, 36.2% had a positive family history. 12.8% also had an allergic disease; none had cancer. The most frequent AI type was Systemic Autoimmune disease (11 case, 23%), followed by Organ-specific autoimmunity (15 cases, 32%), cytopenias (8 cases, 17%), and just antibodies (6 cases, 13%). Other than Autoimmune lymphoproliferative syndrome (ALPS), in which autoimmunity is a case-defining feature, the group of well defined (Hyper-IgE Syndrome (HIES), and Wiskott-Aldrich Syndrome (WAS)) were the PIDs with more cases of autoimmune disease, followed by phagocytosis deficiencies and antibody deficiency. Discussion The overall prevalence of autoimmune disease is relatively high PID syndromes such as ALPS, moderate levels in HIES, WAS and defects of phagocytosis and antibody interestingly. Interestingly, most of our patients with HIES have an autosomal-recessive pattern of inheritance and no identified mutational diagnosis; nearly all of our patients with CGD are receiving chronic subcutaneous therapy with human recombinant interferon gamma. Regular follow-up visits are justified for surveillance for complications and frequent treatment adjustments, given the delicate balance between immunosuppression and infection prophylaxis that is required in the care of these patients.