In this work, the crystalline structure of single crystals grown by vacuum sublimation of unsubstituted palladium phthalocyanines (PdPc), its tetrafluorinated (PdPcF4) and hexadecafluorinated (PdPcF16) derivatives have been investigated using X-ray diffraction measurements. Two crystalline phases have been identified for PdPc; the molecules in both phases crystallize in stacks with herringbone arrangement in the monoclinic space groups (C2/c for α-PdPc; P21/n for γ-PdPc). Both PdPcF4 and PdPcF16 crystallize in the triclinic P-1 space group, forming stacks of molecules in columnar arrangement with molecules in adjacent columns aligned parallel to one another. X-ray diffraction measurements have also been used to elucidate the structural features and molecular orientation of thin films of PdPc, PdPcF4 and PdPcF16, grown by organic molecular beam deposition at different substrate temperatures. The effect of fluorosubstitution on UV-visible optical absorption and vibrational spectra of palladium phthalocyanine derivatives is also discussed.