David Smith, 30, of Aberdeen, New Jersey, who was arrested last week, is charged with interruption of public communications, conspiracy and theft of computer services.
The maximum penalty for the offence is 40 years in prison and a $480,000 fine.
Mr Smith, a former computer programmer, is alleged to have developed the Melissa virus in his apartment.
Melissa clogged e-mail accounts and disrupted computer networks.
The authorities say the virus was named after a topless dancer in Florida.
Mr Smith was freed on $10,000 bail and the case adjourned.
He did not speak to reporters as he left Monmouth County Court, Freehold, NJ.
But his lawyer, Edward Borden Jnr, questioned whether the virus was as destructive as authorities allege.
He said: "Whoever authored the Melissa virus probably is probably more akin to a graffiti artist than an international cyber terrorist."
Country profiles
Melissa virus goes global
(30 Mar 99 | Sci/Tech)
Invasion of the killer e-mail viruses
(31 Jul 98 | Sci/Tech)
International Computer Security Association
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