The present invention relates to a method of loading a sample storage device (10) for a plurality of sample carriers (38A-38E) equipped with sample containers (34), said method comprising: during removal of sample containers (34) from the sample storage device (10): providing at least one output sample carrier (38A) having sample containers (34) that can be taken up from the output sample carrier (38A); providing a target sample carrier (38B) in which sample containers (34) taken up from the output sample carrier (38A) can be deposited; providing a refilling sample carrier (38C) which is at least partially filled with sample containers (34); removing at least one sample container (34) from the output sample carrier (38A) and depositing the at least one sample container (34) in the target sample carrier (38B), and for each sample container (34) removed from the output sample carrier (38A) and deposited in the target sample carrier (38B), removing another sample container (34) from the refilling sample carrier (38C) and refilling the space of the removed sample container (34) in the output sample carrier (38A) with the other sample container (34) from the refilling sample carrier (38C). Moreover, the invention relates to a loading system (12) designed for performing the method.