An automated warehouse system comprising: a storage rack for articles; a transport device (4, 4S) configured to transport an article to the storage rack and transport an article from the storage rack; and a control unit configured to control an operation of the transport device (4, 4S), wherein the control unit includes: a misalignment determination unit configured to determine, after storage of a first article in the storage rack, whether the first article is estimated to have been subjected to vibration exceeding a predetermined threshold value; and a misalignment correction instruction unit configured to, in response to the misalignment determination unit estimating that the first article has been subjected to vibration exceeding the predetermined threshold value, output a control signal to the transport device (4, 4S) to drive the transport device (4, 4S) to perform a misalignment correction operation with respect to a placement position of the first article characterized in that the misalignment determination unit performs the determination by counting the number of times that a second article has been moved to vicinity of the placement position of the first article on a shelf at a level corresponding to the placement position of the article, by counting the number of times that a travel carrier of the transport device travels on a rail on a shelf at a level corresponding to the placement position of the first article, based on a weight of the second article transported by the transport device (4, 4S), or by counting the number of times a lifting platform (4S4) has passed a level corresponding to the placement position of the first article, the transport device (4, 4S) being of a stacker crane type. a storage rack for articles; a transport device (4, 4S) configured to transport an article to the storage rack and transport an article from the storage rack; and a control unit configured to control an operation of the transport device (4, 4S), wherein the control unit includes: a misalignment determination unit configured to determine, after storage of a first article in the storage rack, whether the first article is estimated to have been subjected to vibration exceeding a predetermined threshold value; and a misalignment correction instruction unit configured to, in response to the misalignment determination unit estimating that the first article has been subjected to vibration exceeding the predetermined threshold value, output a control signal to the transport device (4, 4S) to drive the transport device (4, 4S) to perform a misalignment correction operation with respect to a placement position of the first article characterized in that the misalignment determination unit performs the determination by counting the number of times that a second article has been moved to vicinity of the placement position of the first article on a shelf at a level corresponding to the placement position of the article, by counting the number of times that a travel carrier of the transport device travels on a rail on a shelf at a level corresponding to the placement position of the first article, based on a weight of the second article transported by the transport device (4, 4S), or by counting the number of times a lifting platform (4S4) has passed a level corresponding to the placement position of the first article, the transport device (4, 4S) being of a stacker crane type. a misalignment determination unit configured to determine, after storage of a first article in the storage rack, whether the first article is estimated to have been subjected to vibration exceeding a predetermined threshold value; and a misalignment correction instruction unit configured to, in response to the misalignment determination unit estimating that the first article has been subjected to vibration exceeding the predetermined threshold value, output a control signal to the transport device (4, 4S) to drive the transport device (4, 4S) to perform a misalignment correction operation with respect to a placement position of the first article characterized in that the misalignment determination unit performs the determination by counting the number of times that a second article has been moved to vicinity of the placement position of the first article on a shelf at a level corresponding to the placement position of the article, by counting the number of times that a travel carrier of the transport device travels on a rail on a shelf at a level corresponding to the placement position of the first article, based on a weight of the second article transported by the transport device (4, 4S), or by counting the number of times a lifting platform (4S4) has passed a level corresponding to the placement position of the first article, the transport device (4, 4S) being of a stacker crane type.