We have found evidence of molecular vacancies in the herringbone molecular crystals pentacene and hexabenzo[bc, ef, hi, kl, no, qr]coronene using electron diffraction. Experimental electron diffraction patterns taken parallel to the long molecular axis from these crystals exhibited streaking in two characteristic directions, and the streaking approximately followed the molecular herringbone directions. Molecular dynamics simulations of vacancies in pentacene showed that the streaks can be explained by anisotropic lattice relaxations near the defects. Simulated electron diffraction patterns from the crystal-vacancy models at finite temperatures showed streaking similar to the experimental data. The energy of formation of vacancies in pentacene was calculated to be 1.7 eV. The vacancy entropy in pentacene was simulated to be approximately 40 times the Boltzmann constant. We expect these molecular vacancies to influence charge transport and mechanical properties.