An automatic analyzer includes a status table storing the status of each analysis module and reagent information identifying each reagent, the supply of which is exhausted, and allowing tracking of the status of each analysis module, etc. The automatic analyzer determines, based on the status table, whether and how it can continue current analysis, and stores the determination results in its instruction information table. The instruction information table stores analysis-unit or -module operating information and information to be supplied to the user or operator. The analysis-unit operating information includes instructions for the analysis modules to initiate an analysis in a normal manner, finish an analysis in a normal manner, omit a pre-analysis operation, omit a post-analysis operation, or stop sampling, etc. Further, the reagent information and the analysis module status are updated each time a reagent container is replaced by the operator.