Since first being elected to office in 1991, Donoghue has been active on many committees and in various positions. His most significant role to date was that of Chief Deputy Majority Whip, which he has held since 2003. His current committee memberships include the Health and Government Operations Committee (since 2003; including the Insurance Subcommittee since 2004), the Health Insurance and Long-term Care Subcommittees (both from 2003 until 2004), the Pharmaceuticals Subcommittee (in 2005), and the Government Operations Subcommittee (since 2007).