Elizabeth Holmes, the disgraced founder of Theranos, the lab testing company that promised to revolutionize health care, and its former president, Ramesh Balwani, were indicted on 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 start-up. This one boasted a board stacked with prominent political figures and investors, and a startling valuation of $9 billion just a few years ago. In the fabled universe of overnight billionaires and unicorns, companies with billion-dollar valuations, Ms. 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 Ms. Holmes and Mr. Balwani pleaded not guilty to charges of wire fraud. Lawyers for Ms. Holmes could not be reached for comment, but a lawyer for Mr. 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 United States attorney’s office in San Francisco and came about three months after the Securities and Exchange Commission settled civil fraud charges against Ms. Holmes.