Risen won the 2006 Pulitzer Prize for National Reporting for his stories about President George W. Bush's warrantless wiretapping program.

In 2004 Risen came upon information about the National Security Agency's surveillance of international communications originating or terminating in the United States, code-named "Stellar Wind".

He and Eric Lichtblau, who had obtained similar information, co-wrote a story about "Stellar Wind" just before the 2004 United States presidential election.

Bill Keller, Executive editor of the New York Times, and Philip Taubman, Washington Bureau chief, were furious with Risen.

Keller and Taubman negotiated with the Bush administration and, after a delay, the paper published much of Risen and Lichtblau's report about "Stellar Wind" in December 2005.

[2] Risen and Eric Lichtblau were awarded the 2006 Pulitzer Prize for National Reporting for the series of controversial investigative reports that they co-wrote about "Stellar Wind" and about a government program called Terrorist Finance Tracking Program designed to detect terrorist financiers, which involved searches of money transfer records in the international SWIFT database.

In early 2003, The New York Times refrained from publication of the story after an intervention by National Security Advisor Condoleezza Rice with the NYT Executive Editor Howell Raines.

[5] While doing research for the book, Risen's email and phone connections with former CIA Operations Officer Jeffrey Alexander Sterling were monitored by the US federal government.

The New York Times story appeared two days before a former NSA employee, dismissed in May 2005, requested permission to testify to two congressional intelligence oversight committees.

The issue of journalists protecting their anonymous sources was widely discussed during this time period due to the Valerie Plame affair.

[12] In 2011, Risen wrote a detailed response to the subpoena, describing his reasons for refusing to reveal his sources, the public impact of his work, and his experiences with the Bush administration.

[2][19] In an article that Risen co-wrote with Jeff Gerth for The New York Times that appeared on March 6, 1999, they allege that "a Los Alamos computer scientist who is Chinese-American" had stolen nuclear secrets for China.

[20][21][22][23] The suspect, later identified as Wen Ho Lee, pleaded guilty to a single charge of improper handling of national defense information, the 58 other counts against him were dropped, and he was released from jail on September 13, 2000.