Purpose: To investigate the daily setup, interfraction motion, variability in the junction areas, and dosimetric effect in craniospinal irradiation (CSI) patients. Methods: Fifteen CSI patients who had undergone split-field IMRT were followed in the study. Previous, middle, and posttreatment, each target volume position was evaluated using the ExacTrac system. Interfraction and intrafraction motions, the margin of the junction in adjacent targets volumes, and the dosimetric effect of the longitudinal residual error were analyzed. Results: The lowest attainment rate within the tolerance of the initial setup error was 66.79% in six directions. The values of the initial error were within 15 mm (SD 4.5 mm) in the translation direction and 5°(SD 1.3°) in the rotation direction after the transposition of the treatment isocenter. With the guidance of the ExacTrac system, the interfraction and intrafraction residual errors were almost within the tolerance after correction, the margin of CTV-to-PCTV was in the range of target expansion criteria. The residual longitudinal errors resulted in only slight changes in the mean doses of PGTV and PCTV, while the maximum dose of the spinal cord increased by 16.1%. The patients did not exhibit any side-effects by the overall treatment during the follow-up period. Conclusions: Position correction is necessary after setup and the transposition of the treatment isocenter. Intra-fraction motion in the lateral direction should be monitored throughout treatment. The position errors in junction areas are almost within the tolerance after correction. The patients did not exhibit any side-effects by the overall treatment.