Hydra can regenerate its complete adult form from aggregates of dissociated cells. Aggregates of hydra cells are made by dissociating hydra tissue into a suspension of cells and then re-aggregating the cells by centrifugation. An aggregate formed in this way is a disorganized mass of individual cells and does not possess any regeneration polarity. In this study, we analyzed the development of motion in cell aggregates during the regeneration stages in which a new body axis was being established. Two perpendicular diameters (widths) of binalized projection images of an aggregate were continuously measured in order to detect changes in form, i.e., motion. Between 30–35 hr, when the aggregates still appeared spherical, slight motion along a distinct axis was detected along with a simple expansion in the size of the mass. After that, quick twitches along a distinct axis, also seen in intact hydra, began to develop. The axis of the motion corresponded to the future body axis of the regenerated animal, and the future head-end of the body axis showed a larger degree motion than the foot-end. Motion in the aggregates made of cells from hydroxyurea-treated animals in which the stem cells of nerve cells has been eliminated, suggested that the slow one-directional motion observed was due to the epithelial cells, while the twitches were controlled by nerve cells. These results show that the development of motion could provide a useful index to the recovery of organization in the cell aggregates.