Elizabeth Holmes, founder of Theranos, the lab testing company that promised to revolutionize health care, and its former president, Ramesh Balwani, were indicted Friday on charges of defrauding investors out of hundreds of millions of dollars as well as deceiving hundreds of patients and doctors.

The criminal charges were the culmination of a rarity in Silicon Valley — federal prosecution of a technology startup. This one boasted a board stacked with prominent political figures and investors, and a startling valuation of $9 billion just a few years ago. Holmes had catapulted herself and her company into the buzz-filled world of “disrupters” by pledging to upend the health industry and give consumers control over their own care.

Both Holmes and Balwani pleaded not guilty to charges of wire fraud. Lawyers for Holmes could not be reached for comment, but a lawyer for Balwani said in a statement that his client was “innocent and looks forward to clearing his name at trial.”

The indictment was filed by the U.S. Attorney’s Office in San Francisco and came about three months after the Securities and Exchange Commission settled civil fraud charges against Holmes.

On Friday, Theranos also announced that Holmes, who founded Theranos in 2003 as a 19-year-old Stanford University dropout, stepped down as chief executive. She will be replaced by David Taylor, the company’s general counsel.

Holmes and Balwani were accused of misleading the public and their investors by promoting devices and tests that not only did not work but also endangered lives.

Holmes had drafted a spellbinding sales pitch and relentlessly pursued anyone — including her own employees — who doubted her new blood-testing machines.

“This is someone who is so deeply self-deluded by her optimism and faith in herself,” said Paul Saffo, a longtime technology consultant, “and delusion is contagious.”

In addition to misleading investors about the promise of the company, federal officials charged the two with encouraging patients and doctors to use the company’s blood tests despite knowing they “were likely to contain inaccurate and unreliable results.”