The deactivation of one or more cylinders in internal combustion engines has long been established in literature as a means of reducing engine pumping losses and thereby improving brake specific fuel consumption. As down-sizing and down-speeding of modern engines becomes more extreme, drivability issues associated with mode transition become more acute and need to be managed within a suitable calibration framework. This paper presents methodology by which a calibration may be deduced for optimal mode-transitioning in respect of minimising the torque disturbance as cylinders are deactivated and re-activated. At the outset of this study a physics based engine model is used to investigate the key parameters that influence the transition. Having understood these, experiments are designed to establish the level of mode transition disturbance using quantitative statistical indicators such that the cost function may be defined and an optimisation undertaken.The efficacy of the proposed framework is illustrated using a state-of-art engine simulation model that replicates the functionality of a real variable displacement engine. Results show that during mode transition periods the peak torque deviation can be reduced up to five percent of the requested torque. The suggested methodology provides a solution to the mode transition disturbance of variable displacement engines, it is equally applicable in other hybrid/switching powertrain systems where mode transition disturbances are present such as homogeneous charge compression ignition engines and hybrid electric powertrains.