Considering the possibility of long term use of silica aerogels for transparent window insulation materials, we present here the experimental results on the comparison of physico-chemical properties of hydrophilic and hydrophobic silica aerogels. In order to prepare hydrophobic aerogels, the molar ratio of tetramethoxysilane (TMOS) precursor: methanol (MeOH) solvent: water (H2O): ammonium hydroxide (NH4OH) as a catalyst: methyltrimethoxysilane (MTMS) as a hydrophobic reagent was fixed at optimal value=1:12:4:3.6×10−3: 1.3, respectively. After gelation, the aerogels were dried supercritically by high temperature solvent extraction method. It has been found that hydrophilic aerogels (unmodified) adsorbs water ∼4–5 times of its own weight within a time period of 5 min. On the other hand, hydrophobic aerogels (modified) adsorbs ⩽2% water of its own weight even after putting them directly on the water surface for a time period of 1 year. It has been observed that the percentage of optical transmission is quite high (∼95%) in the case of hydrophilic aerogels compared to the hydrophobic silica aerogels (∼80%) at a wavelength of 900 nm for a sample thickness of 1 cm. In order to determine the thermal stability of the hydrophobic nature of the silica aerogels, both hydrophilic and hydrophobic aerogels were heat treated in air, in the temperature range between 25 and 425 °C with a heating rate of 1.5 °C /min. Anomalous weight loss (∼3.3%) has been found in the case of hydrophobic aerogels around 200–210 °C which is the result of thermal decomposition of organic groups. The disappearance of the–CH3 groups was confirmed from IR spectra and 29Si magic angle spinning nuclear magnetic resonance (CP/MAS-NMR) analyses of hydrophobic silica aerogels which were heat treated below and above the threshold temperature (∼200 oC).