Data on preparation and characterization of chitosan-based nanoparticles (NP) carrying small interfering RNA (siRNA) for non-invasive gene therapy is presented. Polyelectrolyte complexation method was carried out in diluted concentrations to obtain relatively small (less than 200 nm) NP. To provide substantial dose of siRNA within tolerable volume of intranasal administration the NP were subjected to enrichment process. Offered here NP fabrication does two steps process comprise provisional and enriched preparations? The differences between these preparations were analyzed with hydrodynamic size distribution and zeta potential measurements. The effect of siRNA lipophilicity on NP physical instability was also tested. Biological evaluation of nanoparticles is described in our published article [1].