A defect in the lipopolysaccharide-responsive beige-like anchor protein (LRBA) gene is a newly defined rare cause of primary immunodeficiency diseases, which manifests as immune dysregulation and humoral immune deficiency. LRBA deficiency is a combined immunodeficiency. A boy with LRBA deficiency is described in this report. He had been diagnosed with Evans syndrome in a haematology clinic. He was referred to an immunology and allergy clinic for frequent respiratory tract infections. He also had hepatosplenomegaly but no lymphadenopathy. Immunological evaluation revealed hypogammaglobulinaemia, increased double-negative T cells, decreased memory B cells and switched B cells, and an inverted CD4/CD8 ratio. LRBA deficiency was considered due to common variable immunodeficiency-autoimmune lymphoproliferative overlap syndrome. A homozygote mutation (c.1964C>T) in LRBA was found through exome sequencing. Gastrointestinal investigation was performed due to unexplained abdominal pain. It revealed atrophic gastritis, partial villous atrophy, and multiple gallstones. There was no chronic diarrhoea or failure to thrive. The abdominal pain disappeared after a cholecystectomy. Multiple gallstones have not been reported in other LRBA-deficient patients who also had autoimmune haemolytic anaemia. Multiple gallstones that require cholecystectomy can develop in LRBA-deficient patients during adolescence.