A cost-effective autofluorescence detecting system has been developed by our research group to diagnose and localize the early gastrointestinal cancer, which is occult to the traditional means of detection, for example, biopsy. At the early stage, we utilize autofluorescence spectrum detected by OMA (Optical Multichannel Analyzer) to discriminate cancerous tissue. Although this method can effectively distinguish tumors from normal tissues, it is not suitable to be applied in clinic use due to the high cost of the-most-often used OMA-autofluorescence detector. Then we designed a novel Double PMTs’(Photomultiply Tube) system, which consists of two parellel-working A/Ds with lower frequency of acquisition, to replace the OMA system, and the results of clinic experiments prove that it can effectively determine gastrointestinal cancers.