Reported emissions data were collated for 35 pharmaceutical-manufacturing installations and 18 power stations holding IPPC licences in Ireland. Consistent and essentially complete sectoral emissions time-series were generated, covering 2002–2006 for the pharmaceutical sector, and 2001–2006 for the electricity-generating sector. Applying the Environmental Emissions Index (EEI) to reported emissions indicated environmental performance improvements of 35 and 30%, respectively, for these two sectors. However, considerable uncertainty was attributed to reporting of heavy metals, NOx and NMVOC emissions at the installation level, and overall NMVOC emissions from the pharmaceutical sector appeared to be considerably under-reported. The fixed average toxicity factor applied to NMVOC emissions in the EEI may deviate from potential temporal changes in the NMVOC compound mix. Overall, reporting uncertainties were found to have a greater impact on EEI outputs than assumptions made in the EEI model, and including an estimate of total sectoral NMVOC emissions reduced the pharmaceutical sector's environmental performance improvement to 24%. The EEI facilitates the comparison and visualisation of reported emissions, integrating them into environmental performance trends. It should optimise interpretation of abundant, detailed, and underutilised ‘bottom-up’ emissions data generated by IPPC installations. For Ireland's pharmaceutical sector, these data are considerably more comprehensive than EPER data.