Epidermolysis bullosa (EB) in neonates is often difficult to characterize, both in terms of making a precise diagnosis and in being able to comment accurately on the prognosis for the affected child. We present a case of a neonate with inherited mucocutaneous fragility and failure to thrive and detail our laboratory approach for classifying the subtype of EB in this child. Mutational analysis revealed a homozygous non-sense mutation in the gene encoding the 180 kDa bullous pemphigoid antigen, also known as type XVII collagen, predicting a non-lethal form of junctional EB. Identification of the underlying molecular pathology in this case was of use in improving diagnosis, classification, management and counselling.