This paper presents results from the ALLEGRO-07 survey that was carried out from 1 to 15 September 2007 across the continental shelf in the Bay of Biscay by the RV "Thalassa". The main objectives were to conduct experiments with a medium-sized, autonomous underwater vehicle (AUV) equipped with a fishery-acoustic scientific payload. This was needed to overcome the difficulties of sampling the surface and bottom blind zones, which are inaccessible to conventional, vessel-mounted transducers used for acoustic surveys in the Bay of Biscay. The AUV acoustic datasets from four dives were compared with those from the research vessel. The results were expressed for the nautical-area-scattering coefficient (sA) and biomass estimates. The AUV provided higher sA measurements than did the vessel. For particular environmental and fish-distribution patterns, the biomass estimated by the AUV was more than ten times that estimated by the vessel alone. The results presented indicate the magnitude of the error that may occur in acoustic surveys, if the biomass in the two blind zones is undetected.