Congenital amegakaryocytic thrombocytopenia (CAMT) is a rare bone marrow failure syndrome characterised by isolated thrombocytopenia because of ineffective megakaryocytopoiesis at birth. In the last 10 years, we collected data from 20 patients diagnosed with CAMT based on a severe thrombocytopenia since birth and absent or markedly decreased numbers of megakaryocytes in the bone marrow. Fanconi's anaemia and thrombocytopenia absent radii syndrome were ruled out for all patients. We retrospectively compared the clinical courses, laboratory findings and treatment outcome. Development of pancytopenia was observed in 14 of the patients, only one patient presented with an isolated thrombocytopenia over a period of over 14 years. One boy died from bleeding complications. We defined two groups of patients according to the course of platelet counts during the first year of life, which also differed in the course of development of pancytopenia. Physical anomalies in addition to haematopoiesis were found in a number of patients: two children presented with cardiac defects, six with growth abnormalities, and four with retardation of psychomotor development. Fifteen patients were treated with haematopoietic stem cell transplantation, four of whom died of transplantation‐related events.