We present VLT-ISAAC spectra at medium resolution of the HH34 and HH46-47 protostellar jets covering diagnostic lines of the ionised ([FeII] 1.644, 1.600 μm) and molecular (H2 2.122 μm) gas. These data have been used to measure the electron density (n e ) and mass ejection flux ( $$\dot{M}jet$$ ) as a function of velocity. In both jets, the electron density is higher in the Low Velocity Component (LVC), although the mass flux is mainly contributed from the High Velocity Component (HVC) that is associated to the large scale jet. In the HH34 H2 Position-Velocity diagram (PVD) the HVC and LVC appear separated suggesting that they may originate from physically distinct regions.