An analysis apparatus includes a first analysis unit which collects samples by utilizing a first nozzle to analyze the sample, a second analysis unit which collects samples by utilizing a second nozzle to analyze the sample, and a transport apparatus which transports a plurality of sample vessels along a predetermined transport route. When a predetermined waiting state is provided such that the transport of the plurality of sample vessels is interrupted or stopped, then the sample collecting position is changed for at least one of the first and second nozzles, and the samples are collected from the plurality of sample vessels by means of the nozzle having the changed position. Accordingly, it is possible to enhance the efficiency of the analysis process performed by the analysis apparatus, while suppressing the transport apparatus from being large-sized and suppressing the structure from being complicated.