This is an introduction to the special issue on cognitive impairments in inherited metabolic diseases (IMD). It provides an overview of the studies included, focusing on the possibility of selective impairments which could provide unique evidence on the specificity of neural circuitries mediating cognitive functions. It will suggest that these circuitries have different metabolic properties which make them especially apt to carry out certain functions, but also particularly susceptible to certain forms of metabolic disruption. Knowledge of selective impairments is also crucial to properly evaluate the difficulties engendered by individual diseases and track treatment outcomes. IMR research holds the promise of a more complete understanding of cognition, from cellular functioning to behaviour and of further improvements in treatment. Advances, however, will require detailed assessments, comparisons across diseases, and the integration of different levels of explanation. This will be possible only through close collaborations between centres and types of professionals.