Venture capital funding in biotechnology companies jumped 46% in the second quarter, as investors looked to replenish their portfolios after an increase in acquisitions and initial public offerings, according to Bloomberg News.

Venture-capital investing across all sectors rose 19% to $7.5 billion in 966 deals, compared with $6.3 billion and 814 deals in the first quarter of 2011, the National Venture Capital Association and PricewaterhouseCoopers said in its quarterly report. The three months ended June 30 represented the biggest quarter for venture funding in two years.

Biotechnology companies attracted $1.24 billion in 116 deals, ranking second behind software makers, who raised $1.52 billion, a 35% jump, in 254 deals. Biotech garnered about $847 million in 97 first-quarter investments. Funding for medical device and equipment makers gained 20% to $841 million in 90 deals.

“We continue to see acquisitions by major pharma and large biotech companies of smaller biotech companies, as well as the return of IPOs to the sector,” Tracy Lefteroff, global managing partner of the venture capital practice at PwC U.S., said in an interview. “For funds that are fortunate to have those exits, that allows them to recycle money and put it into other deals.”

At least 33 U.S. biotechnology companies were acquired during the first half of the year, for a total of $26.7 billion, according to Bloomberg data. The largest deal was Sanofi’s $19.6 billion purchase of Genzyme, completed in April.

The biggest funding in the quarter for the sector was $107 million for Cameron Health, a San Clemente, California-based medical device maker. Close behind were Intrexon, of Blacksburg, Va., receiving $100 million, and Cambridge, Mass.-based Merrimack Pharmaceuticals, which garnered $77 million. Intrexon has also been an active acquirer, purchasing three companies this year.

David Douglass, general partner of Delphi Ventures, which led Cameron Health’s investment round with Alloy Ventures, said FDA regulatory delays for medical devices have pushed firms like his to seek established companies instead of early-stage firms.

“A number of venture firms are starting to want to invest in companies where the pivotal trial has already started, so there isn’t a risk of the FDA delaying the initiation of a trial,” Douglass said yesterday in a call with reporters. “Our investment pace has slowed pretty dramatically over the past two years, because of our concern over the regulatory environment.”