A DNAzyme-mediated target-initiated rolling circle signal amplification strategy based on a microchip platform was developed for detecting apurinic/apyrimidine endonuclease 1 (APE1) at the single-cell level. This strategy was applied to assays of lysate samples from HL-7702, HeLa and MCF-7 cells, with a detection limit of lower than 1 HeLa cell.