To provide a method for amplifying and analyzing a specific nucleic acid fragment containing no sequence artifact by starting cells of the minimum possible number.

This method for amplifying a nucleic acid fragment from a sample or analyzing a microsatellite comprises two or three heat cycle amplification reactions. A primer completely randomized in a first amplification reaction is used and a specific primer is used in a second amplification reaction. In the operation, a mixture of at least two kinds of DNA polymerases is used and at least one of the DNA polymerases has 3'→5' exonuclease activity. In the operation, a sample containing nucleic acid in an amount corresponding to an equivalent to cells more than 100 is used as a sample and an amplified substance of both allelic genes is formed in a probability higher than 90%.