Purpose of review Antiphospholipid syndrome (APS) and systemic lupus erythematosus (SLE) are autoimmune diseases that can affect multiple organ systems. Increased awareness and new treatment strategies ultimately improved the survival of patients, and disease-related comorbidities became more important. The purpose of this review is to focus on comorbidities in these diseases that had a negative influence on the course of the disease. Recent findings There are limited numbers of studies regarding to comorbidities associated with these diseases during childhood. Infections were found to be the most common comorbidity as a result of immunosuppressive agents and dysregulations of the immune system. Other common comorbidities after infections are cardiovascular and cerebrovascular diseases as important causes of mortality and morbidity. In addition, the risk of malignancies, ophthalmologic manifestations, neurologic and renal diseases, musculoskeletal diseases such as vitamin D deficiency, low bone mineral density, and the risk of avascular necrosis were increased in both patient groups. For clinicians, it is important to be aware of the comorbidities that may develop during follow-up of APS and SLE patients. Further studies will shed more light on the comorbidities of these diseases.