Submicron thick polycrystalline pentacene films of different morphology and molecular configuration are prepared by varying the conditions during vacuum deposition on quartz, sapphire and Si substrates. The films are characterized by X-ray diffraction, atomic force microscopy, optical absorption, and Raman spectroscopy. The efficiency of optical second harmonic generation (SHG) is studied as a function of the film properties using picosecond laser pulses at a fundamental wavelength of 1064 nm and femtosecond pulses at a fundamental wavelength of 870 nm. The second-order nonlinearity originates from the lack of inversion symmetry at the surfaces of the crystallites and is practically independent of the structure and morphology of the films. An abnormally low efficiency of SHG from films deposited at room temperature is explained by scattering of the second harmonic at crystals of a size comparable to the wavelength of the second harmonic.