This study investigates the long-term evolution of subtropical ozone profile time series (1999–2010) obtained from ground-based FTIR (Fourier Transform InfraRed) spectrometry at the Izaña Observatory ozone super-site. Different ozone retrieval strategies are examined, analysing the influence of an additional temperature retrieval and different constraints. The theoretical assessment reveals that the FTIR system is able to resolve four independent ozone layers with a precision of better than 6% in the troposphere and of better than 3% in the lower, middle and upper stratosphere. This total error includes the smoothing error, which dominates the random error budget. Furthermore, we estimate that the measurement noise as well as uncertainties in the applied atmospheric temperature profiles and instrumental line shape are leading error sources. We show that a simultaneous temperature retrieval can significantly reduce the total random errors and that a regular determination of the instrumental line shape is important for producing a consistent long-term dataset. These theoretical precision estimates are empirically confirmed by daily i ... mehrntercomparisons with Electro Chemical Cell (ECC) sonde profiles. In order to empirically document the long-term stability of the FTIR ozone profile data we compare the linear trends and seasonal cycles as obtained from the FTIR and ECC time series. Concerning seasonality, in winter both techniques observe stratospheric ozone profiles that are typical middle latitude profiles (low tropopause, low ozone maximum concentrations) and in summer/autumn profiles that are typical tropical profiles (high tropopause, high maximum concentrations). The linear trends estimated from the FTIR and the ECC datasets agree within their error bars. For the FTIR time series, we observe a significant negative trend in the upper troposphere/lower stratosphere of about −0.2%yr−1 and a significant positive trend in the middle and upper stratosphere of about +0.3%yr−1 and +0.4%yr−1, respectively. Identifying such small trends is a difficult task for any measurement technique. In this context, super-sites applying different techniques are very important for the detection of reliable ozone trends.