The diminutive Italian coped admirably in the at times torrential rain at Wentworth Club and at six under par will take a one shot lead into the weekend, ahead of South African George Coetzee, Spaniard Alejandro CaÃƒÂ±izares, England's Mark Foster and Scot Marc Warren.
Molinari's compatriot Matteo Manassero also enjoyed another productive day on the West Course, posting a 71 for a four under par total, the same mark as young English rookie Eddie Pepperell, who provided one of the highlights of the day by birdieing the last four holes.
Molinari said: "I'm really happy with yesterday and today. The conditions were quite tough but I hit the ball well and the putter is working well so I am really happy at the moment.
"Six under is a good score given the conditions - I live over here now so I am used to it - and I'm in a great position going into the weekend, but it's a really tough course so anyone six or seven behind is still in it."
Lee Westwood is well placed at three under par after a second round 71, and said: "My short game's been red hot. When I was walking off the back of the 12th green, where I pitched that shot to about four feet, Ernie (Els) said, 'Bit of a short game wizard now'. If my long game starts to come together, I could be dangerous."
Where Molinari and Westwood made progress, a number of their 2012 Ryder Cup team-mates struggled, as defending champion Luke Donald, Paul Lawrie, Rory McIlroy, Graeme McDowell and Ian Poulter all missed the cut.
Andrew Dodt and Brett Rumford were the only Australians to make the cut, the pair finishing right on the cut mark at 2 over.
Want video tips delivered straight to your inbox? Subscribe to iseekgolf.com newsletters.