A modified shifted-echo PIETA pulse sequence is developed to acquire natural abundance 29Si 2D J-resolved spectra in crystalline silicates. The sequence is applied to the highly siliceous zeolites Sigma-2 and ZSM-12. The 2D J-resolved spectra are used to develop a silicate framework structure refinement strategy based on Si–O, O–O, and Si–Si distance restraints and analytical relationships between local structure and 29Si chemical shifts and geminal 2JSi–O–Si couplings. The refinement of the Sigma-2 structure showed that the Si–O and O–O distances were in excellent agreement with the single-crystal X-ray diffraction (SCXRD) data. The refinement of the ZSM-12 structure, initially determined from synchrotron powder XRD data, highlighted significant improvements in Si–O and O–O distances, and better agreement between calculated and experimental chemical shifts and J-couplings.