A comparison of the ozone data sets from the Stratospheric Aerosol and Gas Experiment II (SAGE II) (version 6.1) and the Halogen Occultation Experiment (HALOE) (version 19) is discussed for the period 1991–2000. A more accurate approach than those used in previous studies is applied for the comparisons, which takes into account measurement uncertainties and produces improved results. This approach gave closer agreement between the two measurement systems in terms of absolute values and differences in long‐term changes, that is, trends determined from each data set. In our work the analysis of weighted mean differences in coincident measurements by the two experiments shows approximately a 5% bias over the altitude range 20.5–50.5 km in the majority of latitude bands, with some exceptions. The SAGE II values are typically larger than the HALOE values. We calculate the slopes of the time series of differences between the two instruments and analyze ozone trends. This analysis, which covers a longer time period than was studied before, indicates little to no long‐term drift in either measurement system. The improved trend analysis methods used in this study show more statistically significant trends than were reported before. Ozone trend comparisons from these instruments show trend differences on the order of less than 0.3% per year in a majority of latitude bands at 25, 35, 45, and 55 km altitudes. Those differences are smaller than reported in other studies, thus revealing remarkable agreement between SAGE II and HALOE trend results.