The Austrian in the VfL Wolfsburg team immediately established himself at the back upon his arrival. Just 70 kms down the road from his former club in Hanover, the central defender has taken up a new challenge and set his sights on reaching the Champions League.

Leadership qualities, aerial strength and a fighting spirit are the new man's trademarks. The presence of the 1.87 meter tall defender's frame is often enough to demand the respect of his opponents.

Born in Graz, Pogatetz's career started at Sturm Graz before going to Kärnten and later to Bayer Leverkusen. After a short loan spell at Aarau, Grazer, and Spartak Moscow, he joined Middlesbrough. He had also been tracked by Fulham, but during his final match on loan at Spartak Moscow, he tackled Yaroslav Kharitonskiy, leaving the Russian with a double leg fracture. On 30 March 2006, during the first leg of Middlesbrough's 2–0 UEFA Cup quarter-final defeat against Basel, Pogatetz broke his nose, jaw and cheekbone in an accidental clash of heads with Mladen Petrić. Retrieved 22 July 2012.

Pogatetz suffered from a hernia, for which he received corrective surgery in Munich on 24 April 2006. On 4 July, he returned to training following successful surgery on his hernia and cheek. In the 2006–07 season, Pogatetz was forced into the centre of defence due to an injury to Chris Riggott. After the 2007–08 season, Pogatetz was given the captain's armband on a full-time basis, following his taking up of the role towards the end of the season.

Pogatetz returned in the 2009–10 season after a long injury layoff, on 7 November in a 0–1 loss to Plymouth Argyle, only to suffer a recurrence of his cheekbone fracture with the scores tied at 0–0. He made his return to the first team against Nottingham Forest on 21 November in a 1–1 draw. He had to wear a protective mask because of his cheekbone fracture which he picked up in the Plymouth game. He received a bang to the head in the Forest game and had to receive stitches at half time, he still completed the full 90 minutes.

On 2 June 2010, he signed for German side Hannover 96 on a three-year contract. On 20 June 2012 Pogatetz signed for the German Bundesliga club VfL Wolfsburg.