Histological assessment of a muscle biopsy is one of the most complex techniques which, currently in the UK, is only provided in very few specialist centres. This requires specialist laboratory skills in handling fresh tissue, freezing under optimal conditions, performing complex histochemical and immunohistochemistry staining on frozen tissue and specialist training for the histopathologists for interpretation and clinicopathological discussion. Access to electron microscopy and Genomic testing is also vital. This review will focus firstly on generic information on clinical indications, specimen handling, panel of histochemical and immunohistochemical stains and histological features of a normal paediatric muscle biopsy. The second section will focus on diagnostic features of a muscle biopsy specifically in the work-up of paediatric neuromuscular and metabolic conditions using case examples. The final section will focus on recent developments in genomic testing and the future prospects of muscle biopsy interpretation. Although complex, muscle biopsy interpretation is mentally stimulating and challenging, and it follows a schematic approach similar to medical liver or renal biopsies. In view of the complexity involved in procuring and handling the sample, muscle biopsy is usually not part of the early stages of work up. This makes it an extremely precious sample, but equally a rewarding exercise when histological interpretation provides the diagnosis and/or guides further genetic testing.