Spots of rain for most of the session meant slick tyres were only used in the final five minutes of FP2.
Four riders didn't set a time, and some didn't return after earlier wet tyre laps.
Pramac Ducati's Loris Capirossi is missing his home event after being injured in qualifying for last weekend's Assen round.
Dani Pedrosa is returning to MotoGP action, after missing the last three races due to a broken collarbone.
The Mugello circuit has been resurfaced for 2011.
for pictures from the grand prix…
Do not copy and paste onto other websites
1. Andrea Dovizioso
ITA Repsol Honda 1m 49.272s
2. Toni Elias
ESP LCR Honda 1m 51.937s
3. Valentino Rossi
ITA Ducati Marlboro 1m 52.550s
4. Alvaro Bautista
ESP Rizla Suzuki 1m 54.497s
5. Randy de Puniet
FRA Pramac Racing 1m 55.279s
6. Karel Abraham
CZE Cardion AB Motoracing 1m 58.334s
7. Hector Barbera
ESP Mapfre Aspar 1m 58.748s
8. Cal Crutchlow
GBR Monster Yamaha Tech 3 1m 59.812s
9. Nicky Hayden
USA Ducati Marlboro 2m 6.386s
10. Hiroshi Aoyama
JPN San Carlo Honda Gresini 2m 9.337s
11. Colin Edwards
USA Monster Yamaha Tech 3 2m 10.026s
12. Ben Spies
USA Yamaha Factory Racing 2m 26.938s
Fastest FP1 time:
ITA Gresini Honda 1m 48.987s
2010 Italian Grand Prix (June 6):
ESP Repsol Honda 1m 48.819s
Fastest race lap:
ESP Repsol Honda 1m 49.531s