An analysis of the effects of using the B-mode ultrasound Acquisition and Targeting (BAT) system for positioning of prostate cancer patients receiving external beam radiotherapy (EBRT) on late gastrointestinal (GI) and genitourinary (GU) toxicity is provided. The records of 49 consecutive patients treated using the BAT were reviewed; additionally, a comparison (No-BAT) group treated in a similar manner was identified, consisting of 49 patients treated immediately prior to this BAT group. There were no other fundamental differences between the two groups. The daily BAT movements were charted and late toxicity was scored for all patients using established toxicity scales. The results demonstrated similar GU toxicity rates between the two groups, but slightly lower rates of GI toxicity in the BAT group vs. the No-BAT group. However, regression analyses revealed that no factors, including BAT use, were significantly correlated with late GI or GU toxicity. Further efforts, perhaps better undertaken in a multi-institutional setting, are needed to determine whether BAT use can significantly reduce late GI toxicity.