Capillary electrophoresis (CE) is the most useful tool for DNA separation because of its high resolution. In this study, different kinds of polymers were used to evaluate the separation efficiency by analyzing a 200-bp DNA ladder. Under optimized CE conditions, the CE separation was performed by DB-17 capillary. The running buffer was a 1 x TBE buffer containing 0.6% w/v poly(ethylene oxide) (PEO) (Mw: 8 000 000) and 1 mu M YO-PRO-1; applied voltage was -10 kV (detector at anode side) and the separation temperature was 25 degrees C. Under these optimal conditions, 15 DNA fragments with sizes ranging from 0.2 to 3.0 kb were resolved within 11.5 min and the RSD of migration time were less than 0.55% (n = 3). This method, combined with three-step multiplex PCR, was applied to detect five alpha-thalassemia deletions, including -alpha(3.7), -alpha(4.2), --(SEA), --(FIL) and --(THAI). A total of 21 patients diagnosed with a-thalassemia were analyzed using this developed method and all results agreed with those already obtained by gel electrophoresis.