A low temperature storage system, a transport mechanism, and a low temperature storage vessel are provided, which enable downsizing and simplification of the transport mechanism, as well as stable transport of stored objects. A low temperature storage system (1) includes a low temperature storage vessel (10) and a transport mechanism (20). The transport mechanism (20) includes a reciprocating part (30) that has a holding part (35) and that is capable of reciprocating along a transfer direction, and guide unit (40). The guide unit (40) include an in-vessel guide (50) fixedly placed inside the low temperature storage vessel (10), and a telescopic guide (60) configured to be able to extend and contract along the transfer direction. The telescopic guide (60) is provided independently of the in-vessel guide (50) so as to be connectable to the in-vessel guide (50).