Diabetes is one of the most common chronic diseases of childhood and adolescence. Type 1, or autoimmune diabetes accounts for more than 95% of cases. Nevertheless, over the past years it has become apparent that not all cases of diabetes presenting in children are autoimmune type 1. In these cases, the diagnosis is facilitated by the fact that many rare etiologies of diabetes are associated with specific clinical syndromes or a characteristic age of onset. In addition, molecular diagnosis is becoming increasingly available for several of these disorders. This review aims to provide the general physician with some important clues to make an accurate diagnosis in these patients and understand its implication in clinical management.