In July 1988, he was appointed by President Reagan's VP, George H. W. Bush to head ADAMHA, the Alcohol, Drug Abuse, and Mental Health Administration, from which he resigned following controversy over his "Violence Initiative" where he used the word "monkey" in the text of one of his slides relating to his comments about inner-city youth and, by making the analogous comparison to primate behavioral studies, how they were prone to similar atavistic behavior due to the prevailing environmental conditions. Even though the term was grossly misinterpreted by the press, the immediate aftermath created a storm of controversy and attacks by other scientists within NIMH, the press and congress which eventually forced Goodwin out as director of ADMHA. After a short time period following the perceived misstep, he was reprimanded in the form of being appointed by then DHHS Secretary Sullivan, to head NIMH, a small step down, from 1992 until resigning in 1994. Goodwin had been on a consistent upward trajectory and had he avoided the controversy, its very possible he could have ascended to director of NIH which was one of his ambitions or even possibly secretary of HHS.
Goodwin published 'Manic Depressive Illness' in 1990 with Kay Redfield Jamison, republished in 2007, which is considered a classic in the field.
Goodwin hosted the award-winning radio show The Infinite Mind. Started in 1997, the show (which at its height aired on over 300 public radio stations throughout the country), won more than 30 journalism awards over 10 years and was considered “public radio’s most honored and listened to health and science program."
Since retiring from government, Goodwin has been actively involved in educating other psychiatrists through continuing medical education (CME) programs and pharmaceutical speakers' bureaus.
An article in The New York Times (Nov. 21, 2008) said that Goodwin had hosted programs that recommended the use of drugs, without disclosing that he had received over a million dollars from their manufacturers.
Goodwin was also on the board of directors of the Center for Medicine in the Public Interest, an "industry-funded front, or "Astroturf" group, which receives a majority of its funding from drug companies." and the radio show was also directly part-funded by pharmaceutical companies which was also not disclosed.
Bill Lichtenstein, the senior executive producer of the show, said that Goodwin had not disclosed payments from pharmaceutical companies, in violation of a strict conflict of interest contract. Goodwin said that Lichtenstein was aware of his educational speaking and consulting activities for pharmaceutical companies, and that in 2005 Goodwin had switched to guest host and let Peter D. Kramer host other shows, including those discussing psychopharmacological treatment, for that reason. An assistant producer of The Infinite Mind independently supported Goodwin's claim. However, 'On The Media' later issued an apology for not contacting Lichtenstein, who reports that when he himself contacted the source she said "she had no knowledge or evidence to support Goodwin's claim...that Lichtenstein or "The Infinite Mind" was aware that Goodwin was being paid to give marketing talks on behalf of pharmaceutical companies". In addition, Lichtenstein points out that Goodwin has told the BMJ (formerly the British Medical Journal) that he didn't believe there had been a conflict of interest, and told George Washington University student newspaper that "I frankly do not see these things as a conflict of interest . . . I've always thought that if you have multiple relationships they sort of cancel each other out".
In 2008, Sen. Charles Grassley (IA-R) conducted investigations regarding possible conflicts of interest between various academic psychiatrists and pharmaceutical companies. Goodwin issued a statement that The New York Times article and the follow-up editorial were filled with misstatements of fact and false implications. Grassley said in regard to a 2008 show in which Goodwin took part: "“After listening to a recording of the show, it appeared to me that the real effect of this particular episode was to undercut any criticism that antidepressants might be linked to an increased risk of suicide."
The Infinite Mind program, which was independently produced and distributed, was slated to end its production at the end of 2008 due to a lack of funding. Nevertheless, following the controversy, NPR cancelled the broadcast of reruns of the show on its Sirius Satellite Radio channel.