In a previous simulation, we demonstrated that the flow induced by a rhythmically expanding/contracting alveolus is highly complex (J. Fluid Mech. 45:245-268, 2000). Based on these earlier findings, we hypothesize that the trajectories and deposition of aerosols inside the alveoli differ substantially from those previously predicted. To test this hypothesis, trajectories of fine particles (0.5-2.5µm in diameter) moving in the foregoing alveolar flow field and simultaneously subjected to the gravity field were simulated. The results show that alveolar wall motion is crucial in determining the enhancement of aerosol deposition inside the alveoli. In particular, 0.5-1µm in diameter particles are sensitive to the detailed alveolar flow structure (e.g., recirculating flow), as they undergo gravity-induced convective mixing and deposition. Accordingly, deposition concentrations within each alveolus are non-uniform, with preferentially higher densities near the alveolar entrance ring, consistent with physiological observations. Deposition patterns along the acinar tree are also non-uniform with higher deposition in the first half of the acinar generations. This is a result of the combined effects of enhanced alveolar deposition in the proximal region of the acinus due to alveoli expansion/contraction and reduction in the number of particles remaining in the gas phase down the acinar tree. We conclude that the cyclically expanding/contracting motion of alveoli plays an important role in determining gravitational deposition in the pulmonary acinus.