We present a multiscale modelling approach to explore the effects of a non-uniform concentration of carbon nanotubes (CNTs) on the electrical conductivity of CNT-polymer composites. Realistic three-dimensional representative volume elements (RVEs) are generated from a two-dimensional CNT concentration map, obtained via microscopy techniques. The RVEs capture the measured probability density function of the CNT concentration and include a length-scale to represent the details of the spatial distribution of the concentration. The homogenized conductivity of the RVEs is computed via multiscale FE analyses for different values of such length-scale, and it is compared to measurements. The modelling strategy is then used to explore the effects of the microstructural features of these materials on their electrical conductivity.