Andrea Dovizioso took a surprise pole position at the Dutch TT while Jorge Lorenzo will have to fight his way through the field following a rain-affected session.
The final practice session on Saturday at Assen was hit by drizzle, leading to several riders suffering falls.
Although the inclement weather died down somewhat in time for qualifying, the conditions still had an impact as Marc Marquez and Maverick Vinales crashed on their out-laps.
Dovizioso, however, adapted to the greasy surface, taking top spot on the grid with a time of one minute and 45.246 seconds.
Ducati's Dovizioso is the first rider not from Movistar Yamaha or Repsol Honda to claim pole this season, with those teams having dominated qualifying since last campaign's Catalan Grand Prix - where Aleix Espargaro topped the timesheets.
Valentino Rossi will start second as the Yamaha man aims to cut his 22-point gap to championship leader Marquez, who qualified fourth behind Scott Redding of Octo Pramac.
Marquez should be confident of extending of stretching his 10-point lead over defending champion Lorenzo, who could only manage 11th place.
Lorenzo will start 10th as Andrea Iannone - who qualified ninth after sweeping both of Friday's practice sessions - drops to the back of the grid as a penalty for his collision with the Spaniard in Barcelona.
Marquez's Honda team-mate Dani Pedrosa equalled his worst qualifying performance, settling for 16th having failed to get out of the first session on his second bike following a crash in practice.