Germans lost many U-boats to the Allied submarine forces during 1939-1945. Several of those were lost with all hands. British submarines were the busiest with 13 kills. 4 U-boats were sunk in the Far East while they served as a part of the Monsun boats there and 5 more were sunk in the Mediterranean sea.
The war at sea was only 3 months old when Germany lost its first U-boat to the British submarine arm when HMS Salmon sank the U-36 outside Kristiansund in Norway.
The U-boats would be lost at a steady rate the entire war with the last one, U-183, being sunk by the USS Besugo on April 23, 1945, only 2 weeks before the German surrender.
Related page
Allied Warships hit by U-boats.
24 boats (1034 total crews, 911 dead, 123 survivors).
* means the boat was sunk with all hands.