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We studied the influence of the fiber orientation on the growth of fiber Bragg gratings (FBGs) in pure silica microstructured optical fibers (MOFs) during femtosecond UV laser inscription. To do so we simulated the transverse coupling efficiency as a function of the relative angle between the inscribing laser beam and the internal microstructure for hexagonal lattice and highly birefringent MOFs by a finite-difference time-domain (FDTD) method. The orientation was predicted to play a far more important role in the highly birefringent MOF. We confirmed these simulation results with the fabrication of wavelength-multiplexed FBG arrays in pure silica core MOFs under different fiber orientations with 266-nm femtosecond laser pulses and a Talbot interferometer configuration.