In the present contribution we assess the total factor productivity (TFP) change in the period 1999-2008 of Swiss dairy farms located in the mountain region using the Malmquist productivity index. We furthermore analyze the robustness of the results of this assessment to the effect of the type of panel used and to different modelling options regarding the inclusion of the ecological and ethological direct payments in the output set. The yearly TFP growth is shown to vary between +1.3% and +3.0% depending on the panel type and modelling option chosen. The results of our work suggest that the TFP growth rate of Swiss dairy farms in the mountain region is not lower than the levels observed in the dairy sector of other European countries. More generally, our investigation shows how sensitive the results of TFP change assessments are to data-related methodological choices and thus highlights the necessity of considering this issue when performing such assessments.