Here we demonstrate that quantum dots (QD) can greatly improve the ultrasensitive capillary electrophoresis-laser induced fluorescence immunoassay of trace anti-benzo(a)pyrene diol epoxide (BPDE)-DNA adducts from sensitivity to separation. We for the first time show that the target QD-antibody-DNA complex is not only effectively separated but also effectively focused by capillary electrophoresis. With the online laser-induced fluorescence detection coupled, the low limits of detection of 6.6 x 10(-21) mol in mass and 120 fM in concentration are achieved for BPDE-DNA adducts. The achieved ultrasensitivity allows for human exposure biomonitoring and shows promising applications of QD in various DNA analyses, including DNA damage.