Since the 1990s, Common Cranes migrating in autumn through Italy have increased significantly both in number and in flock size. In the present study we provided a countrywide profile of autumn crane migration across Italy between 2001 and 2007 (486 records). To investigate the association of climatic characteristics with temporal and spatial migration patterns, we used weather data and climate anomalies over 60 years (1948–2007; NCEP/NCAR Reanalysis Project database). Autumn migration showed different phenological patterns along two main migratory routes: 1) a Southern Italy route and 2) a Northern Italy route. The Southern route, across the lower Adriatic Sea was only partially described before, and more inferred than documented, whereas the Northern route, across the Po River plain, resulted as a new flyway, never described before. Crane migrations along the Northern route occurred 7 to 14 days earlier than along the Southern one. Along both routes, we detected mass migration events concurring with particular weather conditions: the use of Southern route was associated with southward winds in the Balkans, the records along Northern route with high pressure and favourable westward winds in Central Europe and in the main stop-over site (Hortobágy) of likely origin. In the last 60 years, the occurrence of the latter weather configurations has slightly, but consistently, increased, suggesting that the Northern route may have recently established as an alternative route for the cranes migrating from Eastern Europe, joining the two traditional continental routes (the West-European, and the Baltic-Hungarian).