A new method for fast and precise analysis of circle-to-circle amplification (C2CA) products by microchip electrophoresis has been developed. Stable C2CA products were produced by applying a new enzymatic step to C2CA. Detection was carried out within 55s with RSD of migration time of 3.6% (it = 6) enabling reproducibility and high speed. A real sample of bacterial pathogen (V. Cholerae) at single nucleotide level was detected successfully based on this method.