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Inborn errors of metabolism must always be considered in the differential diagnosis of an acutely ill newborn when there is no obvious alternative diagnosis. In addition to a thorough assessment of the medical history and clinical examination of the patient, the diagnosis requires specialised diagnostic testing, including biochemical and molecular tests. The basic diagnostic tests of blood (full blood counts, electrolytes, glucose, acid-base status, creatine kinase, triglycerides, lactate and ammonia), as well as of urine (urine dipstick test for glucose, protein and ketone bodies) will provide a first impression as to whether an inborn error of metabolism may be likely. If such a disorder is suspected, specific metabolic testing should be initiated. Metabolic diseases affect approximately 1% of all newborns in total (i.e. 200 in Slovenia). Most of them remain unrecognised during the neonatal period. A normal result of a screening programme for newborns does not preclude the diagnosis of an inborn error of metabolism, because one can only screen for a limited number of inborn errors of metabolism.