Khatami, 58, arrived at the Interior Ministry registration office on Friday morning wearing his usual black turban and a black cloak over a gray pinstripe robe.
After filling out an application form, he gave an impromptu news conference, promising to continue his reform program if elected for another four-year term.
"I have come to run and I have been faithful to my commitment and to my people and my principles," Khatami said.
"There have been rumors in Iran that I have doubts about running for a second term," he said. "I have had concerns about the future of the revolution and I hesitated to find out in which position I could be more helpful for my country and how I can serve my country."
Khatami, a soft-spoken, habitually smiling cleric, is widely expected to score a comfortable victory in the June 8 polls over conservative opponents who have fought a war of attrition against his campaign to reform the 22-year-old Islamic Republic.
The conservatives are still struggling to find a serious contender to challenge Khatami, still popular despite a series of setbacks since he was first swept to office in 1997.
Confronted by a conservative assault in which key Khatami allies have been removed from office, sympathetic newspapers banned and fellow reformers jailed, Khatami has complained that the presidency lacks the powers needed to reform Iran.
Reformers had accused conservatives entrenched in the judiciary of mounting a campaign to deter Khatami from standing and to weaken his support among the electorate.
Conservatives had accused Khatami of delaying his declaration to undermine their campaign plans.
Officials said Thursday that 134 people, including three women, had so far signed up to run in the election.
Ali Fallahiyan, a staunch hard-liner who has served as intelligence minister, was among those who registered.
Before campaigning begins, candidates will be screened by the conservative-led Guardian Council for their commitment to Islam and the Islamic Republic.
The council is due to announce the results of its deliberations by May 18. Campaigning begins on May 19 and will end 24 hours before the polls open.
Secretary of State Colin Powell said Thursday that talks with Iran can occur only when that makes "some sense," backing away from President Clinton's support of an unconditional dialogue with Tehran.
Powell told a hearing of a Senate Appropriations subcommittee that Iran not only is attempting to produce weapons of mass destruction but also continues to "hang on to an ideology no longer relevant."
Alluding to Iran's weapons program, Powell said, "We will contain them. We will deter them."
The administration has had little to say about Iran since taking office, and Powell addressed the issue only briefly in his testimony.
His comments represented a dparture from the Clinton administration's policy of using the election of moderate leadership in 1997 as a potential springboard for beginning a new relationship with Iran.
Mr. Clinton had called for the opening of an official dialogue with Iran but the appeal fell on deaf ears.
Khatami said that any such talks must be preceded by a dialogue of "civilizations," meaning non-official contacts by religious or other groups.
The State Department has regarded Iran as the world's leading sponsor of international terrorism for the past decade, a designation reaffirmed in the department's latest terrorism report, released Monday.
Other concerns are Iran's efforts to develop biological, chemical and nuclear weapons and to undermine the Middle East peace process.
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