This study used Monte Carlo methods to generate simulations that considered the effort distribution to determine the locations of significant aggregations of cetacean sightings inside the northern Pelagos Sanctuary (north-western Mediterranean Sea). For three years, monitoring has been conducted from five motor vessels covering about 30,050 km. The most frequently encountered species were the striped dolphin Stenella coeruleoalba representing 64.7% of all sightings, the fin whale Balaenoptera physalus (17.0%), Cuvier's beaked whale Ziphius cavirostris (9.9%), Risso's dolphin Grampus griseus (4.3%) and the sperm whale Physeter catodon (2.2%). Sightings' positions and effort coverage were distributed over a grid of 5′ longitude and 5′ latitude. Spatial concentrations of sightings were analysed according to the distribution of effort to identify ‘hotspots’ (locations where the species occurred at a significantly greater frequency than expected), and ‘coldspots’ (locations with a significantly lower frequency than expected). Most fin whale hotspots (14) were located on the bathyal plain between 2000 and 2500 m, four hotspots were around the 1000 m isobaths, and one is located close to the seamount off Genoa. Fin whale coldspots were mainly along the coast. Striped dolphin hotspots were widely distributed over two main areas, in waters with depths between 2000 and 2500 m and at the continental slope; coldspots for this species were also mainly along the coast in the northern part of the study area. Many hotspots were found in the Genoa Canyon, and hotspots of striped dolphins, Cuvier's beaked whales, sperm whales and Risso's dolphins overlapped in this region. Some of the hotspots of Cuvier's beaked whales were identified at the seamount in the study area, where no other species was sighted frequently. Risso's dolphin hotspots were mainly near the 1000 m isobath. For sperm whales, several hotspots were identified: three associated with steep slope features (such as canyons or the continental slope), and one was in the centre of the flat area of Pelagos where the depth is 2500 m. This study highlights the ecological importance of particular locations inside the Pelagos Sanctuary—locations that should be protected from anthropogenic degradations for marine mammal conservation.