Printed electronics on flexible substrates have gained the interest of industry because of their several advantages and applications, such as flexible and lightweight organic LEDs. An inexpensive and simple way to produce them is to print electronic circuits directly on polymer substrates, of which the surface is functionalized with a hydrophilic/hydrophobic pattern to obtain well-defined features. As one of the steps towards such a patterned functionalization, this work investigates the deposition of a hydrophobic thin organosilicon film on poly(ethylene 2,6-naphtalate) (PEN) substrates. The deposition is carried out by means of a parallel plate dielectric barrier discharge (DBD) working at atmospheric pressure, operating with helium as carrier gas and hexamethyldisiloxane (HMDSO) as deposition precursor. The plasma and the deposited film are investigated by means of gas and surface-sensitive diagnostics, respectively, in order to correlate the plasma chemistry to the material properties and to propose a deposition mechanism for the layers under investigation. The hydrophobicity of the film, characterized by means of contact angle measurements, is found to be dependent on the position in the reactor. This is caused by variations in the local plasma chemistry, which causes the film chemistry and morphology to change in the direction of the gas flow. The morphology of the film is investigated by means of atomic force microscopy, while the film chemistry is determined by means of attenuated total reflection Fourier-transform infrared spectroscopy (ATR FT-IR) and X-ray photoemission spectroscopy (XPS). In the direction of the flow, the contribution of methyl groups to the film chemical composition decreases, causing a decrease of the contact angle. Parallel to this change in chemistry, the film surface roughness increases in the direction of the gas flow, which partially compensates the decrease of the contact angle. Overall, the combination of these effects causes a plateau, followed by a decrease, of the contact angle in the gas flow direction. A possible dissociation mechanism for the HMDSO molecule in the plasma is described: yhe dissociation of HMDSO in the plasma is initiated by the scission of a Si-O bond, creating two silicon-containing radicals, or a Si?C bond, creating a methyl radical and pentamethyldisiloxane. The longer HMDSO resides in the plasma, the more methyl groups (low sticking coefficient radicals) are created, decreasing the contribution of methyl groups to the layer and resulting in lower contact angles. Evidence of the removal and further dissociation of methyl groups is found in the optical emission spectra of the plasma, which are recorded at different positions along the reactor.