The existence of framework defects in zeolites, an important class of industrial catalysts and adsorbents, has long been recognized, but little is known about their exact role in zeolite crystallization. Here we show that despite their relatively high framework Al content (Si/Al = 11.5-13.8), as-synthesized PWO, PWW and RTH zeolites, obtained using various trimethylpyridinium cation isomers as organic structure-directing agents (OSDAs) in concentrated fluoride media, contain unexpectedly large amounts of SiO–···HOSi defects which counterbalance the charge of 11-39% of the total OSDA cations occluded per unit cell, but have only a negligible amount (< 0.1 ions per unit cell) of fluoride anions. The results suggest that the phase selectivity of the crystallization in the presence of fluoride ions may be determined by a combination of Al incorporation into the silicate framework, the type of OSDAs used and the microstructure and concentration of SiO–···HOSi defects formed. This study provides a new basis for better understanding the fundamental aspects of zeolite crystallization mechanisms.