How the effects of frequency, tidal volume (VT) and PEEP interact to determine the mechanical properties of the respiratory system is unclear. Airway flow and airway and esophageal pressures were measured in ten intubated, anesthetized/paralyzed patients during mechanical ventilation at 10-30 breaths/min and VT of 250-800 ml. From these measurements, Fourier transformation was used to calculate elastance (E) and resistance (R) of the total respiratory system (subscript rs), lungs (subscript L) and chest wall (subscript cw) at 5, 10 and 0 cm PEEP. As PEEP increased from 0-5 cmH2O, all elastances and resistances decreased (P < 0.05). Increasing PEEP to 10 cmH2O decreased EL, Rrs, and RL further (P < 0.05). The changes in Ers, EL, Rrs and RL caused by PEEP were less (P < 0.05) as VT increased, while changes in Rrs, RL and Ers were less (P < 0.05) as frequency increased. VT dependences in Ers and Rrs were enhanced (P < 0.05) at 0 cmH2O PEEP. The ratio of EL to chest wall elastance was not affected by PEEP (P > 0.05), but increased (P < 0.05) with increasing VT at 5 and 10 cmH2O PEEP. We conclude that it is critical to standardize ventilatory parameters when comparing groups of patients or testing clinical intervention efficacy and that the differential effects on the lungs and chest wall must be considered in optimizing the application of PEEP.