Glass fiber mat filters with deposited silica aerogel layer can serve as low pressure drop filtration media for removing of nanometric particles from gas flow. However such filters are hydrophilic. This reduces their application to environment free of water droplets. A new method of hyrophobization in vapors of TMS was applied. In order to investigate the influence of hydrophobization on filter permeability a series of experimental measurements of permeability to flow of carbon dioxide, nitrogen and helium was performed. The results for both groups of filters were compared.