© 2015 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.We present the SAMI Pilot Survey, consisting of integral field spectroscopy of 106 galaxies across three galaxy clusters, Abell 85, Abell 168 and Abell 2399. The galaxies were selected by absolute magnitude to have Mr <-20.25 mag. The survey, using the Sydney-AAO Multi-object Integral field spectrograph (SAMI), comprises observations of galaxies of all morphological types with 75 per cent of the sample being early-type galaxies (ETGs) and 25 per cent being late-type galaxies (LTGs). Stellar velocity and velocity dispersion maps are derived for all 106 galaxies in the sample. The λR parameter, a proxy for the specific stellar angular momentum, is calculated for each galaxy in the sample. We find a trend between λR and galaxy concentration such that LTGs are less concentrated higher angular momentum systems, with the fast-rotating ETGs (FRs) more concentrated and lower in angular momentum. This suggests that some dynamical processes are involved in transforming LTGs to FRs, though a significant overlap between the λR distributions of these classes of galaxies implies that this is just one piece of a more complicated picture. We measure the kinematic misalignment angle, ψ, for the ETGs in the sample, to probe the intrinsic shapes of the galaxies. We find the majority of FRs (83 per cent) to be aligned, consistent with them being oblate spheroids (i.e. discs). The slow rotating ETGs (SRs), on the other hand, are significantly more likely to show kinematic misalignment (only 38 per cent are aligned). This confirms previous results that SRs are likely to be mildly triaxial systems.