Defect structure of nominally pure lithium niobate crystals grown from a boron doped charge have been studied by Raman and optical spectroscopy, laser conoscopy, and photoinduced light scattering. An influence of boron dopant on optical uniformity, photoelectrical fields values, and band gap have been also studied by these methods in LiNbO3 crystals. Despite a high concentration of boron in the charge (up to 2 mol%), content in the crystal does not exceed 10−4 wt%. We have calculated that boron incorporates only into tetrahedral voids of crystal structure as a part of groups [BO3]3−, which changes O–O bonds lengths in O6 octahedra. At this oxygen–metal clusters MeO6 (Me: Li, Nb) change their polarizability. The clusters determine optically nonlinear and ferroelectric properties of a crystal. Chemical interactions in the system Li2O–Nb2O5–B2O3 have been considered. Boron, being an active element, structures lithium niobate melt, which significantly influences defect structure and physical properties of a crystal grown from such a melt. At the same time, amount of defects NbLi and concentration of OH groups in LiNbO3:B is close to that in stoichiometric crystals; photorefractive effect, optical, and compositional uniformity on the contrary is higher.