Container clearance time is one of the main factors which strongly affects the process of import/export of the country. The time a container spends in a port before clearance is a real cost scenario which will affect the port performance and throughput at all parts of the port. This research aims at studying the operative factors on container clearance in Iranian ports. Achieving this purpose, qualitative factors are converted to quantitative factors, using an empirical-statistical analysis. The results of this research will highlight the problems of container clearance in Iranian ports.