The increase in medical expenses resulting from longer life expectancy is an increasing serious social problem in Japan. Reducing the cost of clinical laboratory systems, increasing quality of service to patients, and safeguarding the health of hospital staff are important issues for hospitals. A flexible clinical laboratory system is needed to reduce system development cost. Automated clinical laboratory systems, for large and small hospitals alike, are needed in order to reduce waiting time and the risk of workers being exposed to infectious diseases. Flexible systems could meet all these needs. We have developed a modularized system architecture to provide a flexible clinical laboratory system. The hardware and software of the clinical and sample transfer equipment are modularized in this system. Each piece of equipment can autonomously decide where to transfer samples and how to process them. The clinical equipment works autonomously and can be added or suspended without influencing the other equipment. The transfer equipment is also autonomous, and the sample transfer lines can be changed easily in accordance with space limitations. We applied this modularized system architecture to a pre-analytical sample-handling system, and demonstrated its effectiveness. This system was developed by using equipment from different vendors, thus demonstrating that such a system can be easily built.