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San Jose has been awarded "Safest Big City in America" numerous times over the last several years.
Most areas in San Jose feel perfectly comfortable walking around after dark. Cities such as Los Gatos, Cupertino, Campbell all feel particularly safe at night.
As with all big cities, you should take care to not leave any valuables on display in your car.
Downtown San Jose, blocks immediately south of San Carlos St along 1st, 2nd and 3rd. These were essentially a "red light" district until they were cleaned up in the 1990's.
The Guadalupe River path from the San Jose Center of Performing Arts to the San Jose Airport, including the Hockey Arena. These neighborhoods used to be rundown and highly traffic'd by homeless people until the 1990's. Lots of new businesses and developments have occurred since, transforming it into nice new park areas, etc.