It is shown, both through simulations and experiments, that the in-line holographic microscopy technique can be used to retrieve very small refractive-index perturbations caused during the filamentation of ultrashort laser pulses. This technique provides the possibility of having spatially and temporally (four dimensions) resolved measurements of refractive-index changes, down to 10−4, from objects with diameters as small as 10 μm. Moreover, we demonstrate the power of the technique in discriminating multiple filaments in a precise quantitative way.