During her time in the county attorney's office, she worked on Family Court and juvenile justice issues.
Pataki won their 1998 election, Donohue was sworn in as Lieutenant Governor of New York on January 1, 1999, replacing Betsy McCaughey Ross.
Since 1999, Donohue started to spend time traveling the state promoting school violence prevention and to implement the recommendations of her task force.
In 2005, Donohue led a state program, comprising several agencies, to determine best practices in the area of school violence prevention.
Part of the recommendations made by Donohue's task force included giving teacher authority to have disruptive students removed from classrooms, creating character education curricula in school districts, and making violence against a teacher in a classroom a felony.
[2] Donohue's task force met around the state to discuss land use policies, economic development, and growth issues.
In that role, she worked with Secretaries of State Alexander Treadwell, Randy Daniels, and Christopher Jacobs on local government issues.
During her second term, Donohue frequently traveled the state promoting homeland security issues, drunk driving prevention, and criminal justice.
In 2005, Donohue was named by Pataki as the Chairwoman of the New York State Delegation to the White House Conference on Aging.
The reports said that either Secretary of State Randy Daniels or Erie County Executive Joel Giambra would replace her on the Pataki ticket.
There were reports that she was offered the Republican nomination for state attorney general to challenge Eliot Spitzer in 2002 so that she would not seek re-election.
In September 2002 Donohue and Pataki fought to win the nomination of the New York State Independence Party.
On March 3, 2006, Donohue informed reporters that her name had been submitted by Pataki to President George W. Bush for nomination to a United States District Court judgeship in Upstate New York.