Main processes which accompany the interaction of energetic particles with the substrate and the growing film in the pulsed laser deposition (PLD) in vacuum are considered. The subplantational film growth mode, which is inherent to PLD, results in the formation of diffuse transition layers (TLs) between the individual materials of the substrate and film. It is argued that thermodynamic forces do not play a significant role in formation of TLs at room temperature by PLD in vacuum, and the resulting concentration profile between the individual materials is determined almost purely by ballistic effects, Up to 10 nm thick TLs in Fe/Al and Ag/Co PLD-produced bilayers have been determined by numerical simulations, semiquantitative analysis and experimentally by means of a quartz thickness monitor. The latter technique has been proposed as an in situ method for determination of TLs between the individual materials with different sputtering yields. The concentration profiles of TLs are featured by a steep slope on the substrate side and an up to 10 nm long tail of the underlying material in the upper layer.