In summary, we have identified a number of environmental exposures, including infectious and non-infectious agents that occurred within 6 months before illness onset, varied by phenotype and may be important in the pathogenesis of JIIM. These findings suggest that a search for a single environmental factor that causes or triggers a single disease as currently defined, such as JIIM, may be unproductive, as patients could have several environmental exposures and these could vary with the disease phenotype that develops. These exposures require confirmation in case-controlled studies to identify whether they are associated with illness onset and whether they play any role in aetiology, yet they suggest focused areas of further research to better understand the environmental factors associated with the onset of JIIM phenotypes and their possible interrelationships with genetic risk factors.