A uniform flow past two unequal sized square cylinders arranged in a side-by-side pattern and at a Reynolds number of 50,000 has been investigated using large eddy simulation (LES) technique. The modelling of sub-grid scales of turbulence is done using the Smagorinsky model. The effect of the transverse gap ratio (T/D) on the flow characteristics has been studied. Numerical simulations are carried out for five different transverse gap ratios (T/D), namely 1.120, 1.250, 1.375, 1.750 and 2.500. Results in terms of the aerodynamic forces, Strouhal number, mean base pressure coefficient, streamlines, vorticity, surface pressure distribution, normal and shear stresses are presented. A shift in the stagnation point for the small square cylinder from the centre of its front face towards its gap side is seen at smaller T/D ratios. The presence of a jet-like flow seen in the gap side is more pronounced at T/D = 1.12. A biased gap side flow towards the near wake of the small square cylinder is seen at smaller T/D ratios. No interference effect is seen at T/D = 2.5. The flow behaviour is similar to that of the isolated square cylinder at this gap ratio. © 2009 Taylor & Francis.