Although fluorescence microscopy is the gold standard tool for biomedical research and clinical applications, their use beyond well-established laboratory infrastructures remains limited. The present study investigated a novel on-chip cell analysis platform based on contact fluorescence microscopy and microfluidics. Combined use of a contact fluorescence imager based on complementary metal-oxide semiconductor technology and an ultra-thin glass bottom microfluidic chip enabled both to observe living cells with minimal image distortion and to ease controlling and handling of biological samples (e.g. cells and biological molecules) in the imaged area. A proof-of-concept experiment of on-chip detection of cellular response to endothelial growth factor demonstrated promising use for the recently developed on-chip cell analysis platform. Contact fluorescence microscopy has numerous desirable features including compatibility with plastic microfluidic chips and compatibility with the electrical control system, and thus will fulfill the requirements of a fully automated cell analysis system.