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Both lysosomal storage diseases and mitochondrial diseases are a group of genetic-inherited metabolic disorders. In an era, where "old fashioned methods" are apparently being replaced by evolving molecular techniques (i.e. exome and whole genome sequencing), the "old fashioned methods" might help to characterise and thus narrow down the potential differential diagnosis. Therefore, we retrospectively evaluated the relevance of electron microscopy of axillary skin for the diagnosis of lysosomal storage or mitochondrial diseases (=inherited metabolic disorders of energy metabolism). Methods and patients: We included 74 patients with developmental delay with regression or neurodegeneration who underwent an axillary skin biopsy for both fibroblast culture and electron microscopy. Because of insufficient skin biopsy quality, for 8 patients no electron microscopy result was obtained. The electron microscopy biopsies revealed abnormalities in 37/66 (56.1%) patients. 29/66 electron microscopy biopsies showed normal results. A definite diagnosis was established in 21/66 (31.8%) patients with a pathological results of axillary skin electron microscopy analysis. In total, in 25/66 (37.8%) of the patients who underwent an axillary skin electron microscopy analysis, a definite diagnosis was finally established. Taking an axillary skin biopsy during anaesthesia or with use of local intradermal lidocaine application is an inexpensive alternative and useful to establish a diagnosis in patients suspected to have a lysosomal storage disease (or inherited metabolic disorder of energy metabolism).