There is provided an automatic analysis system that dispenses samples and reagents into a plurality of reaction vessels to cause reaction and to measure the liquid resulting from the reaction. The system implements a method of handling capped sample containers such as vacuum blood collection tubes along transfer routes. A sample container opening/closing mechanism is provided which removes the caps of the sample containers prior to sample dispensing and which closes the sample containers following sample dispensing using the same corresponding caps as before the dispensing. Also provided is an opening/closing mechanism that retains and manages the caps removed from the sample containers, as well as a transport unit capable of selecting one of the transport routes which fits the identified sample containers so as to close them with the fit caps. This invention thus provides a container opening/closing system that improves throughput of the sample collection process in conjunction with the automatic analysis system performing the sample container opening/closing process.