Abstract For the first time the neutron diffraction study of HZSM-5 zeolites with the general composition of (H1+x)[Al3+xSi4+12-xO24] × wH2O in the orthorhombic approximation (sp. gr. Pnma, z = 8) and initial silicate modules Si/Al = 12, 25, 40 was carried out. As a result, the composition was refined, the distribution of Al3+ ions over the tetrahedral sites (T sites) of the structure was found, and their content in each of them was estimated. It was found that T sites occupation in HZSM-5 structure differ depending on Si/Al, while samples with the same silicate module (Si/Al = 40) obtained under different synthesis conditions differ in the distribution of Al3+ ions over T sites of the structure. It was shown that the calculation of HZSM-5 zeolites crystal structure with substitutions in T sites performed using the VASP 5.2 program with different optimizations (atomic coordinates and unit cell parameters) can only reveal the most thermodynamically energetically favorable sites for Si4+ atoms substitution with other atoms (aluminum and titanium) without predicting their content in each site and regardless zeolite synthesis conditions and type of substituent atom. The relationship between HZSM-5 zeolites catalytic properties and silicate module (Si/Al, Si/Ti) was found and it cannot be ruled out that HZSM-5 catalytic activity is related to Ti4+ ions distribution over the tetrahedral sites of the structure. Graphical Abstract