Provided are a fluorescence generating device and a digital PCR analysis system including the same. The fluorescence generating device includes a clad layer on a substrate, an optical waveguide arranged in a first direction within the clad layer, and a housing which is disposed on the optical waveguide and the clad layer and has a micro fluid channel extending in a second direction. The optical waveguide includes an input waveguide which is provided within one side of the clad layer and provides excitation light to a liquid drop within the micro fluid channel to generate fluorescent light, and an output waveguide which is provided within the other side of the clad layer and has an output inclined surface that reflects the fluorescent light.