Abstract. Variations in the isotopologic composition of water vapour are fundamental for understanding the relative importance of different mechanisms of water vapour transport from the tropical upper troposphere to the lower stratosphere. Previous comparisons obtained from observations of H2O and HDO by satellite instruments showed discrepancies. In this work, newer versions of H2O and HDO retrievals from Envisat/MIPAS and SCISAT/ACE-FTS are compared. Specifically, MIPAS-IMK V5, MIPAS-ESA V8 and ACE-FTS V4.1/4.2 for the common period from February 2004 to April 2012 are compared for the first time through a profile-to-profile approach and comparison based on climatological structures. The comparison is essential for the scientific community to assess the quality of new satellite data products, a necessary procedure to validate further scientific work. Averaged stratospheric H2O profiles reveal general good agreement between 16 and 30 km. Biases derived from the profile-to-profile comparison are around zero between 16 and 30 km for MIPAS-IMK and ACE-FTS comparison. For HDO and δD, low biases are found in the MIPAS-ESA and ACE-FTS comparison in the same range of altitudes, even if associated with a larger de-biased standard deviation. The zonally averaged cross sections of H2O and HDO exhibit the expected distribution that has been established in previous studies. For δD the tropical depletion in MIPAS-ESA occurs at the top of the dynamical tropopause, but this minimum is found at higher altitudes in the ACE-FTS and MIPAS-IMK dataset. The tape recorder signal is present in H2O and HDO for the three databases with slight quantitative differences. The δD annual variation for ACE-FTS data and MIPAS-ESA data is weaker compared to the MIPAS-IMK dataset, which shows a coherent tape recorder signal clearly detectable up to at least 30 km. The observed differences in the climatological δD composites between databases could lead to different interpretations regarding the water vapour transport processes toward the stratosphere. Therefore, it is important to further improve the quality of level 2 products.