Fishways are unnatural environments that typically present fish with uniform depth and lack of cover. Rest and sheltering areas inside fishways may improve retention and overall fish passage. We examined adult Pacific lamprey Entophenus tridentatus use of two specially-designed fishway refuges at Bonneville Dam on the Columbia River (northwestern USA). The 1.1 × 0.4 × 0.2 m boxes provided low-velocity, dimly lit refuges from predation for Pacific lamprey, a largely nocturnal species. The boxes were equipped with antennas to detect lamprey tagged with passive integrated transponder (PIT) tags (n = 3,248 released). In each year of study (2012-2014), 13 – 49% of the PIT-tagged lamprey detected at the fishway exit had used a refuge box. In addition, 63 of 217 (29%) of lampreys double-tagged with PIT tags and radio transmitters detected in the study area used a refuge box. The average residence time of lamprey in the boxes in each year was 49.7 h, 57.2 h, and 52.8 h. There was evidence that lamprey entrance into the boxes peaked at 0300 – 0500 hr and that they typically left the boxes in evening at around 2000 hr. Hence, the boxes probably functioned mostly as a refuge from daylight. Analysis of radiotelemetery data indicated that refuge box users were equally likely to pass over Bonneville Dam as non-users. However, refuge box users were detected less frequently than non-users at sites upstream from the dam, perhaps owing to their longer passage times through our study area (2.0 d versus 0.6 d). While refuge boxes show promise for improving lamprey collection or retention in fishways, further study is needed to ensure that this does not occur at the expense of lamprey fitness.