Abstract: A method for amplifying oligonucleotide in vitro by polymerase-endonuclease chain reaction (PECR) which utilizes a single-stranded DNA probe containing repeat sequences, extends a target oligonucleotide by a thermostable DNA polymerase, cleaves extended products with a thermostable endonuclease, and amplifies target oligonucleotide by thermocycling. In PECR, a specific oligonucleotide is exponentially amplified using one single probe instead of a pair of primers, and the reaction is precisely controlled by thermal cycles whose parameters are flexibly adjustable according to length, sequence, melting temperature and initial amount of the target oligonucleotide. Amplification speed depends totally on initial amount of target oligonucleotide present in the reaction system. The method can be used to amplify specific small nucleic acids, such as oligonucleotides and microRNAs, and further conduct quantitative analysis.