Abstract Background The Western Marsh Harrier (Circus aeruginosus) is a partial migrant with the populations from Eastern and Northern Europe migrating south to sub-Saharan Africa. During the autumn migration, that is peaking in September, harriers move on a broad front heading SW and undertake long sea-crossings en route to their wintering quarters, passing in substantial numbers through Italy and Malta with the highest concentrations recorded at the Strait of Messina. Most of the individuals migrating across the Strait are heading for the wintering quarters in Africa, while fewer spend the winter in Sicily. Methods In a 5-year study (2011‒2015), between 26 August and 30 September, we determined age and sex of autumn migrating harriers through this flyway. In 2014 we determined, by marine radar and optical range finder, the flight altitude of migrating harriers. Results A total of 10,261 Western Marsh Harriers were counted during the whole study, with an average of 2052 per autumn season. Adults outnumbered juveniles and males outnumbered females. Harriers flew at lower altitudes during the morning while large flocks flew lower than single birds or small flocks. Conclusions Our observations are consistent with previous surveys and confirm that adult males have a tendency to migrate over a long distance, while substantial numbers of adult females and juveniles do not head for the wintering quarters in Africa. Finally, flight patterns recorded can be explained by a more pronounced flapping flight of Western Marsh Harriers during migration.