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Wood, 23, carded a 69 at the Pula Golf Club, to stand at nine under, but he will start Sunday's final round with experienced Ryder Cup stars Darren Clarke and Jose Maria Olazabal breathing down his neck.
Clarke is four shots off the pace along with Ireland's Shane Lowry, who matched Gregory Bourdy's course record of 63 from the opening round.
Olazabal is one further back at the course he designed after a 66.
"I have extended my lead by one. I thought that I played pretty well and didn't really get the rewards I deserved," said Wood, who lost a play-off at the Africa Open to British Open winner Louis Oosthuizen in January.
Clarke had two bogeys in his first three holes but struck his approach to the fifth within three feet and made it consecutive birdies at the next.
He holed a 20 footer at the 13th, but three putts on the last saw him sign for a level par 70.
Olazabal, one of a host of players to have attended Seve Ballesteros's funeral on the eve of the tournament, had a bogey at the second but put that behind him with five birdies.
"It's been an extraordinary day on the greens," said the Ryder Cup captain. "I holed many putts and that reflects on the scores.
"I am really happy, four under par is a great score, but I know that I need to keep working.
"I don't remember putting so well in such a long time - I made 23 putts, there aren't many putt days like today. If you play well, everything will come back. My goal is to hit the ball well and if I can do that, results will come. Tomorrow I will go out there and fight like every day."
Leading and selected third round scores at the Iberdrola Open at the Pula Golf Club on Saturday (GBR/IRL unless stated, par 70):
201 - Chris Wood 67-65-69
205 - Shane Lowry 72-70-63, Darren Clarke 65-70-70
206 - Jose-Maria Olazabal (ESP) 71-69-66
207 - Gregory Bourdy (FRA) 63-77-67, David Lynn 68-68-71, Scott Jamieson 67-71-69
208 - Thomas Aiken (RSA) 70-72-66, Alastair Forsyth 68-72-68
209 - Paul Lawrie 68-69-72, Marcel Siem (GER) 70-72-67, Julien Guerrier (FRA) 71-71-67, Simon Thornton 72-65-72, Carlos Del Morral (ESP) 71-68-70, Graeme Storm 71-71-67
210 - Damien McGrane 68-74-68, Peter Whiteford 72-70-68, Danny Willett 64-73-73, Borja Etchart (ESP) 71-73-66, Thomas Levet (FRA) 71-65-74, Bradley Dredge 71-70-69
211 - Martin Wiegele (AUT) 68-70-73, Matthew Nixon 65-70-76, Jorge Campillo (ESP) 71-71-69, Ariel Canete (ARG) 70-68-73, Adrian Otaegui (ESP) 71-73-67, Jason Knutzon (USA) 70-69-72, Pablo Larrazabal (ESP) 69-70-72, Barry Lane 68-73-70, Lloyd Saltman 73-69-69, Cesar Monasterio (ARG) 67-75-69
Selected:
212 - Wade Ormsby (AUS) 73-69-70
213 - Mark Brown (NZL) 73-68-72
215 - Jaco van Zyl (RSA) 67-77-71
216 - Hennie Otto (RSA) 69-70-77
