The present invention relates to a method for analyzing genes using SDL-PCR (separation of displaced ligation probe-based PCR), and more particularly to a method for analyzing genes using SDL-PCR, in which probes comprising a nucleotide sequence complementary to the gene of interest are ligated with each other by ligase, and another probe capable of hybridizing to the probes is hybridized and extended, thereby preparing a template probe, and the template probe for the gene of interest is amplified using universal primers.