Genome analysis using microarrays is increasingly used in genetic testing laboratories to detect clinically significant copy number variants (CNVs). Professional guidelines for this type of testing have been developed in several countries; in general terms, these address mainly practical issues. Although microarray testing provides significant improvements in diagnostic success compared with conventional chromosome analysis by microscopy (karyotyping) the complexities of analysing and interpreting microarray data make the writing of clear, accurate, clinically useful, evidence-based reports challenging. A major impediment is the incompleteness of the human variome, a catalogue of all variation in the genome and its associated phenotypes. Furthermore, it has become clear that CNVs can exert their pathological effects through a wide range of complex genetic and multifactorial mechanisms. The process of evidence-based interpretation is neither clearly defined nor widely understood. The conclusions of research publications in this field are often inferential rather than experimentally tested and the skills needed for thorough assessment are not widespread. Consequently, there is a clear need to incorporate much of this new knowledge into the education and training of the providers and users of microarray reports. These same challenges are also relevant to the emerging use of whole exome and whole genome sequencing which promise comprehensive sequence and CNV detection. There is therefore a need to re-evaluate interpretation and reporting issues and to address this, a forum entitled ‘Microarray Reporting Best Practice Workshop’ was organized by the Genetics Advisory Committee of the Royal College of Pathologists of Australasia. This commentary is the outcome of that discussion.