This paper presents the comparative analysis of the properties of highly dispersed silicas synthesized by pyrogenic and fluoride methods. Raw materials and synthesis conditions differ significantly for the considered methods. The structure and surface properties of synthesized silica samples was characterized by a number of methods such as IR, nitrogen adsorption, SEM, microcalorimetry, temperature programmed desorption time-of-flight with mass-spectrometry (TPDM), thermogravimetric analysis. IR spectra showed presence of characteristic absorption bending bands at 468 сm− 1 (Si-O-Si) and at 800 сm− 1 (O-Si-O) and stretching vibrations bands in the range of 1000–1200 сm− 1 (Si-O-Si) for all the studied samples regardless of their synthesis method. The absorption band at 3750 cm− 1 attributed to free silanol groups ≡ Si-OH confirms the presence of this main sorption centers evenly distributed on the surface for all silica samples. The intensity of this band is quite low for samples obtained by the fluoride synthesis method due to the high water content. This fact is also confirmed by the TGA and TPDM methods. The distribution functions of the activation energy of water desorption demonstrates several maxima: (i) at 60–80 kJ/mol and 100 kJ/mol refers to desorption of molecularly adsorbed water; (ii) at 160–180 kJ/mol is due to the associatively desorbed water. All studied silica samples are hydrophilic according to values of the heat of immersion in water and n-decane, and their Rebinder’s hydrophilicity index Kh > 1. The BET surface area and pore volume of samples significantly depend both on the method of synthesis and on the raw materials.