To provide a gene diagnosis system capable of accurately deciding the presence or absence of a gene even when the amount of a mixed liquid of a reagent and a specimen is changed during examination, and to provide a method for gene diagnosis.

The gene diagnosis system includes a micro-chip having a first detecting part for mixing and reacting a specimen with a reagent, a second detecting part for mixing and reacting a positive control liquid reacting with the reagent to emit fluorescence, with the reagent, and a third detecting part for mixing and reacting a negative control liquid not reacting with the reagent, with the reagent; a fluorescence detecting means for irradiating the first detecting part, the second detecting part, and the third detecting part with excitation light, and outputting a signal corresponding to each fluorescence intensity; a reference value computing means for computing a reference value Vb for deciding the presence or absence of the gene contained in the specimen on the basis of a signal Vp and a signal Vn; and a fluorescence deciding means for comparing a signal Vs with the reference value Vb, and deciding the presence or absence of the gene.