A system analysis apparatus includes a message reconstruction module which reconstructs observed data and data of which the observation has failed, into messages regarding a request and a response which are communicated on a system. The apparatus includes a message candidate extraction module which compares message rules with the reconstructed messages, and extracts messages in the message rules which are identical to the reconstructed messages, from the messages defined in the message rules, as message candidates. The apparatus includes a call relationship extraction module which extracts a call relationship between the message candidates. The apparatus includes a matching module which compares transaction models in which processes in units of transactions on the system have been modeled on the basis of call relationships among the processes on the system, with the extracted call relationship, and selects and determines a transaction model identical to the call relationship.