The 1998–99 French Rugby Union Championship was played by 24 teams divided in the preliminary phase into three pools of 8.

The other played a relegation tournament divided in two pools.

The "best 6th" was Toulon due to having less "red Cards" during the season.

The first of each pools were qualified to quarter of finals Grenoble was 2nd due to having less "red cards" during the season .

Béziers was classified last for worst point difference in the direct matches (Nîmes-Béziers 15–5; 36–37), and was relegated in Pro D2.