Following the launch of the second generation of the A6 station-wagon in 1998, Audi introduced the more powerful version S6 Avant in 1999, along with the S6 Sedan.
The second generation of the Audi S6 Avant was based on the newly-developed C5 platform. It was more than an A6 Avant with different badges. It was offered with more powerful engines and stiffer suspensions that made the car planted to the road. The all-wheel-drive was fitted as standard.

There were some differences between the fierce S6 Avant and a regular A6 Avant. The light-alloy wheels had the design inspired by the Audi TT. The front fenders and the sills were slightly wider. The lowered and stiffened suspension was engineered specially for the S6 range. Two exhaust pipes with chromed tips were fitted as standard on the car. A badge on the grille and one in the back completed the exterior differences.

Inside, the S6 featured high bolstered seats for the front passengers, which ensured better side support on cornering. A set of sport-bucket seats designed by Recaro was on the options list. The rear split-folding bench was kept, just in case something long and heavy had to be delivered fast on the other side of the country.

On the engineering side, the S6 Avant was a completely different car than the rest of the A6 range. The all-wheel-drive system was tuned for performance, with Torsen center differential, and electronic differential locks both front and rear (EDL) managed by the Bosch ESP system. The engine was a 4.2-liter V8 with 340 hp, 40 more than the standard Audi A6 4.2-liter. The car was available with either a 6-speed manual or a 5-speed auto, with manual override for changing gears (Tiptronic).