Objective To investigate the morphological characteristics of the autophagic structures in macrophages after phagocytosis of apoptotic lymphocytes and to explore the effects of autophagy on clearance of the apoptotic cells by macrophages. Methods Apoptosis of lymphocytes was induced with cyclophosphamide. The morphological changes of macrophages phagocytizing the apoptotic cells were viewed with a scanning electron microscope. The structural features of the autophagosome precursors, autophagosomes and autophagolysosomes in macrophages were examined with a transmission electron microscope, and the cross-section areas of the autophagic structures were measured with an image analyzer. The autophagosomes of macrophages were labeled with monodansylcaolaverine(MDC) staining and quantitated using laser scanning confocal microscopy. Results Macrophages actively phagocytized the apoptotic lymphocytes, apoptotic nuclei, apoptotic bodies and other cell debris to form heterophagosomes. When compared with the control group, numbers of autophagic cells and autophagosomes in these cells increase in the group of macrophages that engulfed the apoptotic cells. In addition, the ratios of the cross-sectional areas of the autophagic structures to that of the cytoplasm of the macrophages were greater. There were also apoptotic bodies or other cell debris in many the autophagosomes, and these autophagosomes were large and near the cell membrane. Autophagosomes containing the whole apoptotic cell or apoptotic nucleus were not observed. Conclusion The autophagic abilities of macrophages were significantly enhanced when the cells removed the apoptotic lymphocytes. Autophagy also plays an important direct or indirect roles in clearance of the apoptotic lymphocytes by macrophages.