ATP-binding cassette transporter A1 (ABCA1) promotes the efflux of cellular cholesterol and phospholipids to apoA-I. We described previously a cytoplasmic PEST sequence in ABCA1 and showed that deletion of the PEST sequence results in a prominent increase in the cell surface concentration of ABCA1. In the current study we evaluated the hypothesis that the PEST sequence-deleted ABCA1 might display defective internalization and trafficking to the late endosomes/lysosomes. As assessed by monensin treatment and cell surface biotinylation, the internalization rate of PEST sequence-deleted ABCA1 (ABCA1-dPEST) was markedly decreased compared with wild-type ABCA1 (ABCA1-wt). Immunofluorescence confocal microscopy of ABCA1-wt showed both plasma membrane localization and substantial co-localization with LAMP2 in late endosomes. In contrast, ABCA1-dPEST showed more prominent plasma membrane localization but little co-localization with LAMP2. To assess cholesterol efflux from late endosomes, HEK293 cells were transiently co-transfected with scavenger receptor A (SR-A) and incubated with [3H]cholesterol/acetyl low density lipoprotein (acLDL). Although ABCA1-dPEST showed higher cholesterol efflux than did ABCA1-wt following cell surface labeling ([3H]cholesterol/acLDL in the absence of SR-A co-transfection), it showed impaired cholesterol efflux after late endosomal labeling ([3H]cholesterol/acLDL in the presence of SR-A). Thus, deletion of the PEST sequence leads to a decrease in the internalization of ABCA1 and decreased cholesterol efflux from late endosomal cholesterol pools, providing evidence that the internalization and trafficking of ABCA1 is functionally important in mediating cholesterol efflux from intracellular cholesterol pools.