We report the results of an intercomparison of vertical column amounts of HCl, HF, N2O, HNO3, CH4, O3, CO2 and N2 derived from the spectra recorded by two ground-based FTIR spectrometers operated side-by-side using the sun as a source. The procedures used to record spectra and derive vertical column amounts followed the format of previous instrument intercomparisons organised by the Network for Detection of Stratospheric Change (NDSC), but the level of agreement achieved was significantly better than for previous intercomparisons. For most gases the differences were typically 1% or less, with at least one of the five datasets showing no statistically significant difference between the results from different instruments. Principal exceptions were HNO3 and CO2 when measured on the Mercury Cadmium Telluride (MCT) detectors. For these gases differences of between 2% and 3% were more typical. We present evidence that these larger differences are due to the effects of detector non-linearity and show that by applying an established non-linearity correction method the typical level of agreement can be improved to better than 1% for these gases. We suggest that the improved level of agreement achieved during this intercomparison is indicative of the current state of the art within the NDSC infra-red working group and is a result of improved understanding of the importance of critical alignment parameters and newly developed techniques to characterise the spectrometers’ performance.