Mark Zuckerberg was the big one that got away.

Boston venture capitalists declined to fund the founder of Facebook, the world’s most popular social-networking service, when he wanted to expand his start-up in 2004. Zuckerberg’s move that year to Palo Alto, Calif., from his Harvard University dorm was a wake-up call for New England firms, which have lost market share to Silicon Valley and New York, says Michael Greeley, a general partner at Flybridge Capital Partners.

“There was a little bit of shock that we missed it, as a community,” said Greeley, a board member of the National Venture Capital Association. Since then, Boston “really rallied around ‘how do you let these kids know that the state is open for business and a great place to start companies?’ Sort of a post-Facebook echo boom effect. Zuckerberg should never have left.”

In 2009, Greeley’s firm started Stay in MA, one of several programs designed to entice young entrepreneurs to stay in the region. Incubators such as Dogpatch Labs, started by Polaris Venture Partners, and TechStars Boston offer free space to aspiring entrepreneurs, and angel investors are scouting campuses in search of the next Zuckerberg, Greeley said.

Boston, the birthplace of modern venture capitalism, accounted for 11 percent of U.S. venture investments last year, down from 15 percent in 2003. Silicon Valley firms increased their share to 39 from 34 percent in the same period.

Boston has missed out on much of the recent surge in initial public offerings, driven in part by Internet start-ups. Of $6.83 billion in venture-backed IPOs in the first half of this year, Massachusetts accounted for $209 million, or about 3 percent.

Part of the reason, says Bill Aulet, managing director at the MIT entrepreneurship center, is that Boston’s venture capitalists have traditionally focused on industries that make “real products,” such as software, telecommunications, material sciences and biotechnology.

To be closer to the universities, at least seven firms have opened offices in Cambridge in the past two years.

Spark Capital, an early investor in Twitter and Tumblr, started in downtown Boston. “We were on Newbury Street right in Back Bay, and everyone kind of laughed at us,” said Alex Finkelstein, 35, a general partner. Now, “we’re seeing more of these old-school firms moving from [Route] 128 into Boston or Cambridge because that’s where the entrepreneurs are.”

Facebook — turned down by Battery Ventures and MetroPCS — is valued at $82.4 billion on SharesPost, a secondary exchange for shares of private firms.

Boston area firms missed out on the social networking boom in part because many didn’t grasp its significance, said Howard Anderson, a senior lecturer at the MIT Sloan School of Management and co-founder of Battery Ventures. He said the average angel investor in Boston is about 55 years old. In California, the average is 32, he said. “It became a generational issue,” he said. “To understand things like Facebook, you have to be 19 to 24 years old. If you’re 56, you don’t quite get it.”

Many venture capitalists in the Boston area cringe at the implied valuations of some Internet companies. At its current valuation, Facebook would be worth 59 percent more than Ford Motor, the second-largest U.S. automaker, and more than twice as much as BlackRock, the world’s largest asset manager. Groupon, the coupon site, has an implied valuation of $10.4 billion, said SharesPost, but had revenue of just $713 million last year. In comparison, discount retailer Dollar Tree has a market value of $8.5 billion and sales of $5.9 billion.

“For people who say this is not a bubble,” Anderson said, “I reminded them that 10 years ago they were saying, ‘It’s different this time.’ And it never was.”

Fifty-three Internet companies have filed for U.S. IPOs this year, versus 164 companies in 2000. By contrast, just three biotech companies have filed for IPOs, down from 46 in 2000.

LinkedIn, based in Mountain View, Calif., saw its shares more than double in value May 19, its first day of trading. The stock has been little changed since.

Greylock Partners, founded in 1965, moved its headquarters to Menlo Park, Calif., from Waltham. It was an early backer of LinkedIn, Facebook and Pandora and a recent investor in Groupon.

Apart from Silicon Valley, New York has been among the biggest beneficiaries of the shift in venture capital. New York is home to consumer Internet start-ups such as Gilt Groupe, Foursquare Labs and Tumblr, a microblogging site.

Venture investments in companies in the New York metro area totaled $580 million in this year’s first quarter, or 10 percent of the total nationwide, compared with $639 million in the New England region, which had an 11 percent market share.

Greeley cited a “historic frustration” that schools like MIT and Harvard educate students only to see them leave. Cambridge has the highest number of people with doctorates per capita in the nation.

“We tend to focus on things that are hard and novel,” Greeley said. “The novelty of Facebook was the social outlet, it wasn’t the technical insights.”

Andrew McCollum, part of the original Facebook team, said there is much more excitement now about entrepreneurship at Harvard, and in the city, than when he left the school in 2006.

“It was just really amazing, the difference in the environment and enthusiasm,” said McCollum, 27, who is entrepreneur in residence at Flybridge. “CS50, the intro computer science class, is now one of the biggest courses at the school.”

Finkelstein says people who were skeptical of Spark’s investments in Tumblr and Twitter a few years ago don’t laugh now. Twitter is raising funding that values the company at about $7 billion.

“We invested in Tumblr when it was a one-person company, Twitter when it was a 15-person company,” he said. “A lot of people thought we were crazy for those investments when we made them, and now the valuations speak for themselves.”