The analysis apparatus for microchips, each at least having a main flow path performing migration of a sample for analysis inside a sheet-like member, comprises a holding part holding microchips so that the multiple main flow paths are provided; a pretreatment part common to the multiple main flow paths for performing a pretreatment step prior to an analysis step in each of the multiple main flow paths; a processing part for performing analysis in each of the main flow paths independently of the others; and a control part controlling an operation in the pretreatment part so that when a pretreatment step for one main flow path ends, a pretreatment for a next main flow path starts and further controlling an operation in the processing part so that an analysis is subsequently performed for the main flow path where the pretreatment step has ended.