Background: Benign prostatic hyperplasia (BPH) is a common disease among older men and many patients with prostate cancer (PC) also have BPH. External beam radiation therapy (EBRT) is one of the important treatments for PC, nevertheless, few studies have analyzed the effect of BPH on EBRT. We tried to know the risk of bladder toxicity by analyzing the bladder volume variability in patients with BPH. Materials and Methods: Changes in prostate location with respect to the presence of BPH and bladder volume by bladder zone were analyzed. Dosimetric parameters of prostate and bladder were analyzed using planning computed tomography (CT) scans in 20 patients with PC. Three planning CTs were performed on each patient during RT. Maximum bladder volume variations were calculated using the three planning CT scans and volumes of upper and lower zones were compared. Results: Mean upper and lower bladder volume ratio was 0.85 and 0.15, and mean maximum differences in bladder volumes for the three CTs were 97.33 cc and 10.36 cc for upper and lower bladders, respectively (p < 0.001). Prostate size and location with respect to prostate upper margin showed a moderate linear correlation (r = 0.567, p = 0.009). Prostate superior margins of patients with or without BPH were located at mean distances of 3 mm above and 4.8 mm below the superior border of pubic bones, respectively (p = 0.019). Conclusion: The prostates of patients with BPH were more likely to be located in the upper bladder zone, which exhibited greater bladder volume variability. This implies that the clinical target volume of EBRT is located in an unstable bladder zone, which would decrease treatment accuracy and increase treatment-related bladder toxicity. The further clinical study is required to analyze the relation between BPH and the severity of RT-induced bladder toxicity.