Pulmonary alveolar proteinosis has traditionally been treated with whole-lung lavage (WLL). The literature describes a variety of techniques used in performing the WLL, including mechanical vs manual chest percussion, use of prone positioning, and variances in lavage volume. We have quantified and compared the effective alveolar clearance for each component of the lavage by measuring the dry weight of material in the lavage effluent. We measured this in five patients who underwent six consecutive WLLs at the University of Pittsburgh Medical Center. We performed the lavage in the following three stages: stage I, passive drainage; stage II, assisted clearance; and stage III, positional clearance. Aliquots of lavage effluent were centrifuged to determine the dry weight of material present in sequentially recorded bottles within each stage. At the initiation of each augmentation, there was a statistically significant improvement in the clearance of material (stage II, p = 0.009; stage III, p = 0.012). Furthermore, we show that lipoproteinaceous material is present in the lavage effluent in all stages of latter portions of the lavage. The effective removal of material would be expected to have an impact on the physiologic and clinical response to WLL. This finding emphasizes the importance of performing an adequate and standardized lavage.