A simple and fast method for electrochemical detection of amplified fragments by PCR was successfully developed using CE in a microfluidic device with a modified screen-printed carbon electrode (SPCE). The surfaces of the SPCE were modified with poly-5,2'-5',2''-terthiophene-3'-carboxylic acid, which improves the analysis performance by lowering the detection potential, enhancing the S/N characteristics, and avoiding electrode poisoning. DNA fragments amplified by PCR were separated within 210 s in a 75.5 mm-long coated-separation channel at a separation field strength of -200 V/cm. To minimize the sample adsorption into the inner surface of the capillary wall, which disturbs the separation, a dynamically coated capillary with an acrylamide solution was used. Furthermore, the analysis procedure was simplified and rendered reproducible by using 0.50% w/v hydroxyethylcellulose as a separation matrix in a coated channel. The reproducibility of the analysis employing the coated channel yielded RSD of 4.3% for the peak areas and 1.4% for the migration times in eight repetitive measurements at a modified electrode, compared with 21.3 and 9.4% for a bare electrode. The sensitivity of the assay was 18.74 pAs/(pg/microL) with a detection limit of 584.31 +/- 1.3 fg/microL.