Novartis has kicked off 2010 with a pharmaceuticals mega-merger and may end up paying nearly $50 billion for eye-care company Alcon, at least on paper.

The Swiss-based firm bought a 25% stake in Alcon in 2008 for $10.4 billion and is now exercising its option to pick up another 52% stake from Nestle for $28.1 billion. In addition, Novartis is offering to buy out minority shareholders – who hold the remaining 23% of shares – by giving them Novartis shares worth $11.2 billion.

“The addition of Alcon will strategically strengthen our healthcare portfolio and our position in eye care, a sector with dynamic growth due to the increasing patient needs of an aging population,” says Daniel Vasella, chairman and CEO of Novartis (press release).

“… It will also allow us to strengthen innovation power by combining R&D efforts and grow our global market presence thanks to our complementary product portfolios.”

Novartis says there will be “integration-related workforce reductions” – otherwise known as lay-offs – as it seeks to save around $300 million over three years from the total merger, but it did not say where these would occur. Vasella also says that there should not be large job cuts as there will also be jobs created by the merge (Reuters).

The company is offering $180 per share for the 52% Nestle stake but only $153 for the 23% minority state. A number of commentators think it will have to raise its offer to the minorities.

“I don’t think they’ll get the rest of the shares for that price,” David Kaegi, an analyst at the private bank Sarasin, told the Wall Street Journal.

The billion-dollar deal follows a busy December for pharma companies. C&EN has a round up of the major deals and The Motley Fool has a run down of the generic drugs which will go off patent this year, a factor which is driving much of the manic merging.