A single service break in the second set was enough for Xavier Malisse of Belgium to beat defending champion and top-seeded Ferrer in straight sets, 7-6 (3), 6-3.
"I think I need to play more on grass to get into it," Ferrer said.
"I can now train for a few days in London. I have to stay positive; my focus is now on my first match at Wimbledon."
Ferrer was the top but far from the only seeded player to fall in the first round of the men's draw.
Second-seeded Stanislas Wawrinka bucked the trend by beating Steve Darcis 7-6 (5), 6-4. Darcis was a late replacement for Dutchman Igor Sijsling, who dropped out of the tournament in the morning with a stomach complaint. The only other seeded player to reach the second round was Jeremy Chardy of France, seeded fifth, who beat Lucas Pouille 7-5, 6-4.
The top-seeded woman, 2011 champion Roberta Vinci, had no such problems, brushing aside Kaia Kanepi 6-3, 6-3 in the first match on center court to reach the second round.
Fourth-seeded Kirsten Flipkens rallied from a set down to overcome Francesca Schiavone 3-6, 6-3, 6-0 in the first round while Carla Suarez Navarro advanced to the quarterfinals by beating Sofia Arvidsson 6-3, 6-4.
Benoit Paire was another seeded player who didn't make it past the first round, retiring after losing the first three games of the match to fellow Frenchman Michael Llodra.
Results from day three of the Hertogenbosch ATP/WTA Open (x denotes seeding):
Men:
First round:
Lu Yen-Hsun (TPE) bt Edouard Roger-Vasselin (FRA) 6-1, 7-6 (7/3)
Michael Llodra (FRA) bt Benot Paire (FRA x4) 3-0 ret'd
Jeremy Chardy (FRA x5) bt Lucas Pouille (FRA) 7-5, 6-4
Xavier Malisse (BEL) bt David Ferrer (ESP x1) 7-6 (7/3), 6-3
Nicolas Mahut (FRA) bt Ricardas Berankis (LTU) 6-1, 6-4
Jan Hernych (CZE) bt David Goffin (BEL) 6-3, 3-6, 7-6 (7/4)
Marius Copil (ROM) bt Rogrio Dutra Silva (BRA) 6-7 (4/7), 6-4, 6-2
Stanislas Wawrinka (SUI x2) bt Steve Darcis (BEL) 7-6 (7/5), 6-4
Women:
First round:
Roberta Vinci (ITA x1) bt Kaia Kanepi (EST) 6-3, 6-3
Lesya Tsurenko (UKR) bt Daniela Hantuchova (SVK) 5-0 retired
Kirsten Flipkens (BEL x4) bt Francesca Schiavone (ITA) 3-6, 6-3, 6-0
Second round:
Carla Suarez (ESP x3) bt Sofia Arvidsson (SWE) 6-3, 6-4
Tsvetana Pironkova (BUL) bt Irina Begu (ROM) 7-6 (9/7), 6-2
Urszula Radwanska (POL x7) bt Magdalena Rybarikov (SVK) 4-3 retired