A cell processing system comprising: a first processor (100, 200) connectable to a source container filled with a biological fluid, the first processor (100, 200) comprising: a separator configured to separate the biological fluid from the source container into at least two streams of material (46, 48); and a first container configured to receive one of the at least two streams along a first fluid pathway; a second processor connectable to the first container, the second processor comprising: a magnetic separator configured to select target cells, the target cells being associated with magnetic particles; a second, pass-through container associated with the magnetic separator, the second container connected at a first end to the first container along a second fluid pathway; and a third container connected to a second end of the pass-through container; and one of the first processor (100, 200) and the second processor comprising at least one pump configured to transfer material between the separator and the first container along the first fluid pathway, and between the first container and the second container along the second fluid pathway; and at least one controller coupled to the first processor (100, 200) and the second processor characterized in that the second end of the pass-through container is connected only to the third container, and the third container is a waste container. a first processor (100, 200) connectable to a source container filled with a biological fluid, the first processor (100, 200) comprising: a separator configured to separate the biological fluid from the source container into at least two streams of material (46, 48); and a first container configured to receive one of the at least two streams along a first fluid pathway; a separator configured to separate the biological fluid from the source container into at least two streams of material (46, 48); and a first container configured to receive one of the at least two streams along a first fluid pathway; a second processor connectable to the first container, the second processor comprising: a magnetic separator configured to select target cells, the target cells being associated with magnetic particles; a second, pass-through container associated with the magnetic separator, the second container connected at a first end to the first container along a second fluid pathway; and a third container connected to a second end of the pass-through container; and a magnetic separator configured to select target cells, the target cells being associated with magnetic particles; a second, pass-through container associated with the magnetic separator, the second container connected at a first end to the first container along a second fluid pathway; and a third container connected to a second end of the pass-through container; and one of the first processor (100, 200) and the second processor comprising at least one pump configured to transfer material between the separator and the first container along the first fluid pathway, and between the first container and the second container along the second fluid pathway; and at least one controller coupled to the first processor (100, 200) and the second processor characterized in that the second end of the pass-through container is connected only to the third container, and the third container is a waste container.