The purpose of this study was to quantify the relationship between treatment time and dose uncertainty due to intrafraction organ motion in prostate cancer radiotherapy (RT). Ten consecutive patients with prostate cancer treated by radical RT by volumetric modulated arc therapy (RapidArc) were considered. For each patient, pre- and post-treatment cone beam computed tomography (CBCT) was performed in 10 fractions. The prostate, rectum and bladder were contoured on each CBCT. The change in organ position, volume and dosimetric uncertainty induced by organ motion were evaluated. Interval time between the two CBCTs ranged between 4 and 16 min (mean 7.3 ± 0.7 min). Treatment with intrafraction prostate motion >3mm and > 5 mm were 24% and 5%, respectively. Regarding change in centroid position and volume, a poor time correlation was found for target and rectum, while a constant increase was obtained for bladder. The agreement index was highly correlated to time (r = -0.89 for bladder, r = -0.95 for rectum, and r= -0.84 for prostate). In terms of difference in dose volume histogram between pre- and post-CBCT, the dose uncertainties for the targets and rectum amplified with the increasing time. The increasing intrafraction dose uncertainty with time requires the use of an RT technique with minimization of treatment time to improve confidence in planning dose distribution.