Abstract: We quantify the impact of massive neutrinos on the statistics of low-density regions in the intergalactic medium as probed by the Lyman alpha forest at redshifts z = 2.2-4. Based on mock but realistic quasar (QSO) spectra extracted from hydrodynamic simulations with cold dark matter, baryons and neutrinos, we find that the probability distribution of weak Lyman alpha absorption features, as sampled by Lyman alpha flux regions at high transmissivity, is strongly affected by the presence of massive neutrinos. We show that systematic errors affecting the Lyman alpha forest reduce but do not erase the neutrino signal. Using the Fisher matrix formalism, we conclude that the sum of the neutrino masses can be measured, using the method proposed in this paper, with a precision smaller than 0.4 eV using a catalogue of 200 high-resolution (signal-to-noise ratio similar to 100) QSO spectra. This number reduces to 0.27 eV by making use of reasonable priors in the other parameters that also affect the statistics of the high-transitivity regions of the Lyman alpha forest. The constraints obtained with this method can be combined with independent bounds from the cosmic microwave background, large-scale structures and measurements of the matter power spectrum from the Lyman alpha forest to produce tighter upper limits on the sum of the masses of the neutrinos.