Read our latest coverage of patent law and intellectual property issues, from Silicon Valley to the U.S. Supreme Court.

“Many inventors filing patent applications planned on submitting their papers today, which would have been the last opportunity to do so under the PTO’s old rules,” said James Gatto, a Pillsbury partner who heads the firm’s IP practice. “The court’s action today gives inventors and their attorneys more time to plan and file for patents, while the future of the PTO’s new rules remain in question.”

Glaxo filed its suit against the U.S. Patent and Trademark Office and its director, Jon Dudas, earlier this month. The company plans to seek a permanent injunction.

In a 39-page opinion handed down late Tuesday, Judge Cacheris sided with Glaxo’s lawyers at Kirkland & Ellis. He agreed there probably would be irreparable harm to Glaxo if the injunction weren’t granted. The company has about 100 pending patent applications that would be affected. Cacheris said the new rules tilt the balance of hardships unfairly toward Glaxo, and might in general be harmful to the public interest.

“I think it’s an indication of a relatively weak position by the PTO, at least with regard to at least some aspects of the rules,” said Ted Apple, a patent prosecutor with Townsend and Townsend and Crew in Palo Alto.

Many patent prosecutors say they hope the injunction will cause the patent office to reconsider the new rules.

“I hope that this will be an opportunity for the patent office to develop a more workable set of rules for the patent applicant community,” said Hans Troesch, a veteran patent prosecutor with Fish & Richardson in Palo Alto.