An automatic analyzer for executing an analytical reaction requiring two or more temperature changes in the process of sample preparation, comprising: a plurality of reaction containers capable of containing samples and reagents; a plurality of incubation mechanisms capable of controlling the temperatures of the reaction containers and set at two or more different temperature levels; a transport mechanism for transporting the reaction containers; an analytical mechanism for analyzing the samples contained in the reaction containers, wherein the automatic analyzer is adapted, in the process of sample preparation, to transport the reaction containers in a given order by the transport mechanism to the incubation mechanisms in which two or more different temperature levels are set and, in the process of analysis, to assay analytical reactions by the analytical mechanism; and a control mechanism for controlling the transport mechanism, wherein the transport mechanism is controlled to transport each reaction container from one to another of the plurality of incubation mechanisms so that its temperature is changed, characterised in that when different assays are executed with two or more sample containers, the transport mechanism is controlled by the control mechanism to transport reaction containers to a given incubation mechanism in a given order in accordance with the assay to be performed on the sample in each sample container, and the control mechanism alters the duration during which a reaction container containing a sample is regulated by each incubation mechanism depending on the temperature of the sample in the reaction container before its transportation to the incubation mechanism. a plurality of reaction containers capable of containing samples and reagents; a plurality of incubation mechanisms capable of controlling the temperatures of the reaction containers and set at two or more different temperature levels; a transport mechanism for transporting the reaction containers; an analytical mechanism for analyzing the samples contained in the reaction containers, wherein the automatic analyzer is adapted, in the process of sample preparation, to transport the reaction containers in a given order by the transport mechanism to the incubation mechanisms in which two or more different temperature levels are set and, in the process of analysis, to assay analytical reactions by the analytical mechanism; and a control mechanism for controlling the transport mechanism, wherein the transport mechanism is controlled to transport each reaction container from one to another of the plurality of incubation mechanisms so that its temperature is changed, characterised in that when different assays are executed with two or more sample containers, the transport mechanism is controlled by the control mechanism to transport reaction containers to a given incubation mechanism in a given order in accordance with the assay to be performed on the sample in each sample container, and the control mechanism alters the duration during which a reaction container containing a sample is regulated by each incubation mechanism depending on the temperature of the sample in the reaction container before its transportation to the incubation mechanism.