Aims. We present a new continuum 3D radiative transfer code, MCFOST, based on a Monte-Carlo method. MCFOST can be used to calculate (i) monochromatic images in scattered light and/or thermal emission, (ii) polarisation maps, (iii) interferometric visibilities, (iv) spectral energy distributions and (v) dust temperature distributions of protoplanetary disks. Methods. Several improvements to the standard Monte Carlo method are implemented in MCFOST to increase efficiency and reduce convergence time, including wavelength distribution adjustments, mean intensity calculations and an adaptive sampling of the radiation field. The reliability and efficiency of the code are tested against a previously defined benchmark, using a 2D disk configuration. No significant difference (no more than 10%, and generally much less) is found between the temperatures and SEDs calculated by MCFOST and by other codes included in the benchmark. Results. A study of the lowest disk mass detectable by Spitzer, around young stars, is presented and the colours of “representative” parametric disks are compared to recent IRAC and MIPS Spitzer colours of solar-like young stars located in nearby star forming regions.