The deformation of a lattice of hexagonal-packed cylinders has been correlated to the applied oscillatory strain via time-resolved simultaneous small-angle X-ray scattering (SAXS) and rheology experiments. Kraton-type poly(styrene)-poly(ethylene-co-butylene) poly(styrene) (PS-PEB-PS) triblocks were pre-aligned in the hexagonal-packed cylinder phase formed in the melt. Specimens were then subjected to oscillatory strain (7%, i.e. small but in the non-linear viscoelastic regime) with the cylinder axis parallel or perpendicular to the shear axis at room temperature (where PS is glassy). At the same time, SAXS was used to probe the change in domain spacing during one cycle of shear with a time resolution down to 2 ms. It was found that the lattice deforms in phase with the applied strain (although the stress is out-of-phase). However, the deformation is not affine. The observed change in domain spacing for the cylinders was significantly smaller than the applied strain for both the perpendicular and parallel orientation. The deviation from affine behaviour was greatest for the parallel orientation. This non-affine behaviour is ascribed to the take-up of strain by initially poorly oriented grains. Rheology data obtained concurrently with the SAXS indicates a two-step relaxation of the dynamic shear modulus, The initial fast process may be due to the realignment of grains, whereas the slower process may be due to the perfection of lattice order resulting from non-linear viscoelastic strains.