We discuss the bounds on the cosmological lepton number from Big Bang Nucleosynthesis (BBN), in light of recent evidences for a large value of the neutrino mixing angle theta13. The largest asymmetries for electron and muon or tau neutrinos compatible with 4He and 2H primordial yields are computed versus the neutrino mass hierarchy and mixing angles. The flavour oscillation dynamics is traced till the beginning of BBN and neutrino distributions after decoupling are numerically computed. The latter contains in general, non thermal distortion due to the onset of flavour oscillations driven by solar squared mass difference in the temperature range where neutrino scatterings become inefficient to enforce thermodynamical equilibrium. Depending on the value of theta13, this translates into a larger value for the effective number of neutrinos, N_eff. Upper bounds on this parameter are discussed for both neutrino mass hierarchies. Values for N_eff which are large enough to be detectable by the Planck experiment are found only for the (presently disfavoured) range sin^2(theta13)<0.01.