Avoidance of approaching vessels by fish is a major source of uncertainty in surveys of fish stocks. In an effort to minimize vessel avoidance, international standards for underwater-noise emission by research vessels have been established. Despite widespread investment in noise-reduced vessels, the effectiveness of noise reduction on vessel avoidance remains poorly understood. Here, we report on vessel comparisons of pollock abundance recorded by the NOAA ships "Oscar Dyson" (OD), a noise-reduced vessel, and "Miller Freeman" (ME), a conventionally designed vessel. The comparisons were made during three acoustic surveys of prespawning aggregations of walleye pollock (Theragra chalcogramma) in Alaska. The experiments demonstrate that a noise-reduced vessel will detect significantly more fish backscatter than a conventional vessel in some situations. OD detected 31% more pollock backscatter than MF in the Shumagin Islands, where pollock were distributed between 100 and 200 m deep, and 13% more pollock backscatter in Shelikof Strait, where pollock were primarily distributed 200-300 m deep. However, there was no difference in the Bogoslof Island area where pollock were found at 400-700 m. In the Shumagin and Shelikof areas, the discrepancy between vessels tended to decrease with fish depth, consistent with a decreasing response to a stimulus propagating from the surface. Analysis of the depth distributions of pollock supports the conclusion that the discrepancies in backscatter stem from differential behavioural responses to the two vessels.