In this study we propose an automatic reading system for diagnostic DNA chips. We define a general specification for an automatic reading system and propose a possible implementation method. The proposed system performs the whole reading process automatically without any user intervention, covering image acquisition, image analysis, and report generation. We applied the system for the automatic report generation of a commercialized DNA chip for cervical cancer detection. The fluorescence image of the hybridization result was acquired with a $GenePix^{TM}$ scanner using its library running in HTML pages. The processing of the acquired image and the report generation were executed by a component object module programmed with Microsoft Visual C++ 6.0. To generate the report document, we made an HWP 2002 document template with marker strings that were supposed to be searched and replaced with the corresponding information such as patient information and diagnosis results. The proposed system generates the report document by reading the template and changing the marker strings with the resultant contents. The system is expected to facilitate the usage of a diagnostic DNA chip for mass screening by the automation of a conventional manual reading process, shortening its processing time, and quantifying the reading criteria.