A method of handling a reagent container in an automatic analyser enabling automatic replacement of a reagent during analysis comprising the steps of: requesting an analysis by an operator; confirming whether a reagent container to be used for the analysis exists on a reagent driving disk; if the reagent container to be used for the analysis is not set on the reagent driving disk, confirming whether a vacant position is present on the reagent driving disk; characterised by: if no vacant position exists on the reagent driving disk but a vacant position exists on a fixed disk, moving by means of a reagent container moving unit one reagent container from the reagent driving disk to the fixed disk in order to make the vacant position on the reagent driving disk; if no vacant position exists on either of the reagent driving disk and the fixed disk, moving by means of the reagent container moving unit one reagent container from the reagent driving disk to a loading system in order to make the vacant position on the reagent driving disk; and if a vacant position exists on the reagent driving disk, moving by means of the reagent container moving unit a reagent container containing the reagent to be used for the analysis from the fixed disk onto the vacant position of the reagent driving disk. requesting an analysis by an operator; confirming whether a reagent container to be used for the analysis exists on a reagent driving disk; if the reagent container to be used for the analysis is not set on the reagent driving disk, confirming whether a vacant position is present on the reagent driving disk; characterised by: if no vacant position exists on the reagent driving disk but a vacant position exists on a fixed disk, moving by means of a reagent container moving unit one reagent container from the reagent driving disk to the fixed disk in order to make the vacant position on the reagent driving disk; if no vacant position exists on either of the reagent driving disk and the fixed disk, moving by means of the reagent container moving unit one reagent container from the reagent driving disk to a loading system in order to make the vacant position on the reagent driving disk; and if a vacant position exists on the reagent driving disk, moving by means of the reagent container moving unit a reagent container containing the reagent to be used for the analysis from the fixed disk onto the vacant position of the reagent driving disk. if no vacant position exists on the reagent driving disk but a vacant position exists on a fixed disk, moving by means of a reagent container moving unit one reagent container from the reagent driving disk to the fixed disk in order to make the vacant position on the reagent driving disk; if no vacant position exists on either of the reagent driving disk and the fixed disk, moving by means of the reagent container moving unit one reagent container from the reagent driving disk to a loading system in order to make the vacant position on the reagent driving disk; and if a vacant position exists on the reagent driving disk, moving by means of the reagent container moving unit a reagent container containing the reagent to be used for the analysis from the fixed disk onto the vacant position of the reagent driving disk.