Advances in the diagnosis and treatment of inborn errors of metabolism (IEM) have aroused renewed interest in these diseases in recent years. The vast degree of complexity involved in this pathology requires a great amount of effort in its diagnosis and, on many occasions, the need to resort to complex complementary examinations that can only be performed in specialised reference centres. AIMS. To review and outline the clinical features and diagnostic methods by drawing up a protocol to be followed in an attempt to offer care to these patients. Development and conclusions. We propose a diagnostic schema divided into three levels: the first level is based on the patient record, age at onset, and the signs and symptoms, which will enable us to establish the clinical suspicion of the type of IEM. On the second diagnostic level, the foregoing information is taken into account in order to decide whether it is advisable to carry out certain basal confirmatory tests in order to establish groups of biochemical patterns that allow us to get closer to an aetiological diagnosis. We believe that these basal tests should be available in most hospitals. A third level refers to employing specific diagnostic methods which are frequently carried out in reference centres. We also review metabolic encephalopathies that are associated to epilepsy and psychomotor or mental retardation due to their being the most common reasons for visits related to IEM in Neuropaediatric units.