In 2009 Henry Samueli was a founding director of the Broadcom Foundation, a 501c(3) corporate nonprofit, and he is the chair of this philanthropy that advances science, technology, engineering and math (STEM). Broadcom Foundation sponsors the Broadcom MASTERS (Math, Applied Science, Technology and Engineering for Rising Stars) and the Broadcom MASTERS International, programs of Society for Science and the Public that inspire middle school students to continue math and science courses into high school in order to create pathways to STEM careers. Samueli was inspired by his own seventh grade experience of building a short wave radio from a Heathkit for innovation that he funded the Marconi/Samueli Award for Innovation with his Marconi Award. Henry and Susan Samueli also sponsor the top prize, the $25,000 Samueli Foundation Prize in the Broadcom MASTERS.
16 months later, on December 10, 2009, Judge Carney, after hearing the testimony of all the witnesses at the trial of CFO William Ruehle, dismissed the case against Samueli (as well as Ruehle and Nicholas), citing Samueli's testimony as well as prosecutorial misconduct. In his ruling Judge Carney stated "The uncontroverted evidence at trial established that Dr. Samueli was a brilliant engineer and a man of incredible integrity. There was no evidence at trial to suggest that Dr. Samueli did anything wrong, let alone criminal. Yet, the government embarked on a campaign of intimidation and other misconduct to embarrass him and bring him down." He further added in his ruling "Needless to say, the government’s treatment of Dr. Samueli was shameful and contrary to American values of decency and justice." The judge ordered Dr. Samueli's plea agreement to be "expunged" from his record and stated "Dr. Samueli now has a clean slate."