We simulate non-linear behaviour of soils during strong ground motion in the Rhône valley in southern Switzerland. Previous studies of the site response using weak ground motion, ambient noise and linear 3-D FD simulations suggest that the 2-D structure of the basin will lead to amplification factors of up to 12 in the frequency band between 0.5 and 10 Hz. To estimate the importance of non-linear soil behaviour during strong ground motion in the Rhône valley we simulate the response of a superficial soft layer with a fully non-linear 1-D finite difference code. The non-linear wave propagator is based on an effective stress constitutive soil model capable of predicting pore pressure evolution due to shear. We determine the required dilatancy parameters from laboratory analysis of soil samples using cyclic triaxial tests. In order to include the effect of the strong 2-D structure in our non-linear analysis synthetic seismograms are convolved with the transfer function of the basin and then propagated through a 1-D non-linear layer. We find that reduced amplification due to soil non-linearity can be expected at rock accelerations above 0.5 ms-2, and that de-amplification occurs at ground motion levels of approximately 2 ms-2. Nevertheless, the spectral accelerations simulated forthe valley centre are still exceeding the design spectra at about 0.5 Hz for magnitudes above 6.0, which reflects the strong amplification of ground motion by the deep 2-D resonance of the basin. For frequencies above 1 Hz the design spectra are generally in agreement with the strongest simulated accelerations. We evaluate the occurrence of soil failure using the 5 per cent strain criterion as a function of hypocentral distance and magnitude. Results confirm observations of liquefaction reported after the 1855 Mw 6.4 earthquake of Visp, and they suggest that soil liquefaction may occur at distances beyond those predicted by empirical relations in the valley. Near the basin edge, however, the simulated liquefaction occurrence agrees with the empirical relations. These results suggest that the response of the whole structure needs to be simulated in order to estimate the non-linear seismic response of complex basins like the Rhône valley