Elan has quietly given Johnson & Johnson the right to acquire its 49.9 percent stake in their joint Alzheimer’s disease venture, a move that could deter potential bidders for Elan and which has riled some shareholders, Reuters reports.

The agreement, which is buried in Elan’s recently filed annual report, is part of a broader deal announced last July in which J&J agreed to pay $1 billion for 18.4 percent of Elan and take a 50.1 percent stake in a new company working on Elan’s experimental Alzheimer’s drugs, Reuters continues.

The terms were revised after it was disclosed Elan and J&J reached a secret agreement in which J&J could gain 50 percent in the Tysabri multiple sclerosis drug, which Elan markets in a 50-50 partnership with Biogen Idec. As it turns out, Elan not only gave J&J an option on Tysabri, it also gave J&J an option to acquire its 49.9 percent stake in a subsidiary formed by J&J to acquire Elan’s Alzheimer’s Immunotherapy Program (AIP), which includes bapineuzumab, an experimental drug.

“Many large shareholders are up in arms about this,” said Larry Feinberg, who runs Oracle Investment Management and holds 5 million Elan shares, tells Reuters. “Elan has one of the best neuroscience businesses in the world, but now Biogen has right of first refusal on Tysabri and J&J has right of first refusal on bapineuzumab. It’s something that will get in the way of a potential acquirer.”

Karen Andersen, an analyst at Morningstar, says the agreement should have been reported last summer. “I think this is material information,” she tells Reuters. “I think this should have been volunteered and discussed when they had their conference calls to discuss the deal, rather than putting us in a position of digging for it later.”

Biogen, whose standstill agreement with Elan expires in June, is considered the most logical suitor for Elan. That’s because each company has the right to acquire the other’s share of Tysabri should there be a change of control at either company, Reuters notes.

Elan acknowledged its bapineuzumab deal with J&J could also prove daunting. “We are party to agreements that may discourage a takeover attempt that might be viewed as beneficial to our shareholders,” the company writes in its annual report, listing the newly revealed Alzheimer’s drug agreement with J&J as an example. Elan did not directly respond to Reuters when asked why it didn’t disclose this agreement when the transaction was announced.

You may recall that last yaer, a federal court judge ruled Elan breached its contract with Biogen, prompting Elan to withdraw the Tysabri option from its deal with J&J. In response, J&J cut the amount it would pay for its Elan stake by $115 million to $885 million, Reuters reminds us.