Spin coaters are the essential instruments in micro-fabrication processes, which apply uniform thin films to flat substrates. In this research, a spin coater diagnosis system is developed to detect the abnormal operation of TFT-LCD process in real time. To facilitate the real-time data acquisition and analysis, the circular-buffered continuous data transfer and the short-time Fourier transform are applied to the fault diagnosis system. To determine whether the system condition is normal or not, a steady-state detection algorithm and a frequency spectrum comparison algorithm using confidence interval are newly devised. Since abnormal condition of a spin coater is rarely encountered, algorithm is tested on a CD-ROM drive and the developed program is verified by a function generator. Actual threshold values for the fault detection are tuned in a spin coater in process.