| Rank | Rider | Points |
|---|---|---|
| 1 | 61 | |
| 2 | 45 | |
| 3 | 44 | |
| 4 | 33 | |
| 5 | 33 | |
| 6 | 26 | |
| 7 | 25 | |
| 8 | 18 | |
| 9 | 14 | |
| 10 | 13 | |
| 11 | 12 | |
| 12 | 12 | |
| 13 | 10 | |
| 14 | 10 | |
| 15 | 9 | |
| 16 | 8 | |
| 17 | 5 | |
| 18 | 5 | |
| 19 | 4 | |
| 20 | 4 | |
| 21 | 3 | |
| 22 | 3 | |
| 23 | 2 | |
| 24 | 2 | |
| 25 | 2 | |
| 26 | 2 | |
| 27 | 2 | |
| 28 | 1 | |
| 29 | 1 | |
| 30 | 1 | |
| 31 | 1 | |
| 32 | 1 |
Info
Pantani, the strong leader, had a huge lead and seemed unbeatable. However, on the morning of the penultimate stage, he was disqualified from the Giro after a blood test showed an elevated hematocrit, which was seen as a sign of doping. Subsequent investigations and revelations suggested that the Neapolitan mafia may have played a role in falsifying his blood results to force him out of the race, as they would otherwise have suffered losses.
| Date | 05 June 1999 |
| Start |  Madonna di Campiglio |
| Finish | Aprica |
| Distance | 190.0 km |
| Type | Individual Road Race |
| Average Speed | 31.92 km/h |
| Overall Profile | Mountain |
| Finish Profile | Mountain |