The effect of fluoride presence in a synthesis mixture on the parameters of the fine structure of SBA-15 has been studied. The amount of fluorides, the addition stage and the duration of the hydrothermal stabilization of the structure have been varied. Fluoride addition during SBA-15 synthesis increases the material formation rate and decreases the ordering duration of the highly organized mesostructure. During hydrothermal treatment under conventional conditions, fluorides cause a restructuring of the micropore system. There is micropore merging into relatively large coalesced micropores inside the silicate wall, that are practically undetected by t-plot or alpha-S methods due to the high ratio of the pore diameter to its length. The addition of fluoride results in a decrease in the thickness of the silica wall and an increase in the mesopores diameter as well as the cell parameter of the final product.