The commission voted 4-2 to limit when and how the groups, known as 527s, can use corporate and union money for election activities.
Since the passage of the McCain-Feingold campaign finance reforms were approved, a number of groups indicated they would try to use their status outside the two-party system to circumvent the restrictions.
"Today's ruling effectively shuts down illicit 527 groups that operate in the shadows by using unregulated soft money to influence federal elections," Gillespie said.
The commission, he added, "...should be commended for its campaign finance ruling to uphold the new law of the land."
Gillespie called the ruling "the beginning of true campaign finance reform" and invited Democrats "to join us in welcoming a more transparent and accountable era in American politics."
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