Reactor grade plasmas are likely to be fuelled by pellet injection. This technique transiently perturbs the profiles, driving the density profile hollow and flattening the edge temperature profile. After the pellet perturbation, the density and temperature profiles relax towards their quasi-steady-state shape. Microinstabilities influence plasma confinement and will play a role in determining the evolution of the profiles in pellet fuelled plasmas. In this paper we present the microstability analysis of pellet fuelled H-mode MAST plasmas. Taking advantage of the unique capabilities of the MAST Thomson scattering system and the possibility of synchronizing the eight lasers with the pellet injection, we were able to measure the evolution of the post-pellet electron density and temperature profiles with high temporal and spatial resolution. These profiles, together with ion temperature profiles measured using a charge exchange diagnostic, were used to produce equilibria suitable for microstability analysis of the equilibrium changes induced by pellet injection. This analysis, carried out using the local gyrokinetic code GS2, reveals that the microstability properties are extremely sensitive to the rapid and large transient excursions of the density and temperature profiles.