A formal intercomparison of atmospheric total column measurements of N2O, N2, CH4, O3, HCl, HNO3, and HF by two ground-based solar Fourier transform infrared (FTIR) spectrometers conducted as part of the Network for the Detection of Stratospheric Change (NDSC) instrument certification procedure at Lauder, New Zealand, is presented. The two instruments were nominally very similar, collocated, and collected data at the same times. Collected spectra were analyzed independently by the individual operators in a blind-phase intercomparison, then reanalyzed by a single operator using identical analysis methods to eliminate any potential bias from the spectral analysis. From the consistent reanalysis, gases with predominantly tropospheric distributions and pressure-broadened spectral lines, such as N2O and CH4, showed differences between retrieved columns of typically less than 1%. For predominantly stratospheric gases, such as HCl and O3, differences were less than 3%. In most cases, the differences were greater than the scatter in the individual measurements and were significant at the 95% confidence level. The worst case observed was for HF, which showed a 7% systematic bias between instruments. The differences are consistent in magnitude with those expected for known types of imperfection in spectrometer alignment and operation, but attempts to quantify these effects through instrument line shape analysis, phase error, zero offsets, and channel spectra did not remove the apparent differences.