Sklyarov is facing charges that he trafficked and conspired to traffic in tools designed to circumvent copy control technologies, an action made criminal under the DMCA. If convicted, Sklyarov could serve up to 25 years in prison, and would also be subject to a fine of up to $2.25m (£1.6m).
Sklyarov's employer, Moscow-based software firm ElcomSoft, was also indicted by the same grand jury and could be fined as much $2.5m (£1.7m). A representative of the company entered a plea of not guilty.
A hearing has been set for 4 September.
The Electronic Frontier Foundation (EFF) has opposed Sklyarov's prosecution since his arrest, the first criminal prosecution under the DMCA. The group's legal director, Cindy Cohen, commented: "This debate should not be happening in a criminal trial when a man's life is at stake."
Sklyarov is the author of Advanced eBook Processor, an application that decrypts Adobe Systems eBook Reader format e-books, and allows them to be printed, copied, backed up and resold. Adobe eBook Reader files normally do not have those capabilities. Sklyarov was arrested in July after Adobe complained about Advanced eBook Processor to the US Department of Justice.
The case has sparked worldwide protests in the weeks since Sklyarov's arrest. Protestors have called for his release and charged that the DMCA is unconstitutional, that it abridges free speech and that it puts an end to the fair use doctrine, a traditional consumer right that allows for sharing, trading and limited copying of copyrighted works.
About 30 protestors gathered outside Boston Public Library to make speeches and hand out leaflets about Sklyarov's case.
C. Scott Ananian, student and organiser of the Boston protests said, Sklyarov's indictment "just makes us more determined".