As Merck & Co. Inc.'s new head of R&D, Roger Perlmutter plans to refocus and prune the pharma's pipeline of 31 Phase II and Phase III programs. But with half of its Phase III programs near completion, the real evidence of his handiwork may not be visible for another three to five years.

Merck has struggled more than many of its pharma peers to fill the gap left by patent expirations for blockbuster drugs due to late-stage discontinuations and regulatory setbacks. Among its seven programs in registration, Merck has received complete response letters for three, including one request for additional trials. Additionally, since June 2011, Merck has discontinued three programs after large Phase III trials were complete.