Alzen established himself through Porsche single-make racing in Germany, winning the 1992 Porsche Carrera Cup Deutschland and then the 1994 Porsche Supercup. In 1995 he claimed the privateer B-Class championship in the Deutsche Tourenwagen Meisterschaft (DTM).
In 1996 Alzen graduated to the full Deutsche Tourenwagen Meisterschaft International Touring Car Championship, driving an Opel Calibra V6. When that series was discontinued, he raced for Opel in the German Super Tourenwagen Cup.
The 1999 season produced the most contentious episode of his career. Alzen appeared to have won the Super Tourenwagen Cup championship for Opel under circumstances that became fiercely disputed. In the deciding final-round incident, his Opel teammate Roland Asch crashed into title rival Christian Abt. Alzen, leading the race, collided with Abt's teammate Kris Nissen and limped to second. Weeks after the season, an amateur video emerged proving that Asch had deliberately crashed into Abt. The championship was stripped from Alzen and awarded to Abt instead.
Alzen moved to the new Deutsche Tourenwagen Masters (DTM) with Opel in 2000 but was released from the team following a collision with teammate Manuel Reuter. He later drove for AMG-Mercedes in the DTM and departed that team in 2003 under similar circumstances.
Away from touring cars, Alzen compiled a strong record in international sports car competition. In 1998 he won the GT1 class at the 24 Hours of Daytona, driving a Rohr Motorsport Porsche 911 GT1 Evo. That same year he competed in the FIA GT Championship season and at the 24 Hours of Le Mans in a Porsche 911 GT1, finishing second overall at Le Mans. In 2004 he returned to FIA GT competition, sharing a Vitaphone-sponsored Saleen S7 with Michael Bartels.
In January 2012, Alzen was confirmed for a full American Le Mans Series season, sharing a BMW with Jörg Müller.
Away from major championship racing, Alzen and his elder brother Jürgen became a celebrated pairing at the Nürburgring Nordschleife. From 2003 to 2005 they competed in the VLN Endurance Racing Series and the 24 Hours Nürburgring in a privately built Porsche 996 GT2 Turbo 4WD. Uwe set a Nordschleife lap record with the car at 8 minutes 9 seconds — roughly ten seconds faster than the contemporary factory DTM cars from Opel and Audi and the BMW M3 V8 GTR of Schnitzer Motorsport. The Alzen brothers also took pole positions against those works teams. In the 2005 24-hour race, however, electronic problems prevented them from starting in wet conditions.
For 2006, rule changes led the brothers to switch from the turbocharged engine to a naturally aspirated Porsche 997 GT3. They chose to run a standard H-pattern manual gearbox rather than the sequential unit, judging the sequential version would not survive the full race distance. The car finished second behind a Manthey Porsche that used a sequential gearbox saving several seconds per lap — a result Uwe publicly lamented after the race.
Nürburgring fans voted Alzen their Driver of the Year for 2004.
In 2008 Alzen entered the Speedcar International Series with Phoenix Racing, winning two races and finishing third in the overall standings.
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