Normal mucociliary transport in the mucoperichondrium of the nasal septum is from a distal (anterior) to proximal (posterior) direction. This study was to determine the direction of mucociliary transport and histopathological changes in nasal mucosal rotation flaps when their transport directions were anatomically reversed. Thirty-two rabbits were divided into four groups. Surgical septal rotational flaps were prepared in the experimental groups. Group I was the control group. The distal aspect of the flap was sutured through a large septal window to the other side of the nasal septum, thus changing the direction of the flap. Evaluation was performed 1 week, 1 month and 9 months later with each of these groups named as groups II, III, and IV, respectively. The rate and direction of the mucociliary transport was determined and histopathological investigations were performed from the flaps. The direction of mucociliary transport was observed to continue as distal to proximal direction in the rotated segments. The mucociliary transport rate was found to be decreased in group II, nearly normal in group III, and in normal limits in group IV after surgery. Intense inflammation and decreased number of cilia were present in group II. The inflammation was milder in group III and the epithelium was found to be nearly normal in group IV. The originally programmed direction of mucociliary transport in the nasal rotation flaps is maintained and is not altered or reprogrammed. Histopathological changes revert back to normal from an inflammatory state to reach pre-surgical status over time.