The judge concluded the case last week, saying that "... the defendants have infringed claims 1, 3 and 5 of the 031 patent, that those claims are valid, and that the 031 patent is enforceable.
"Accordingly, this case will proceed to the second phase trial to decide the issues of willfulness and damages."
But despite the positive outcome, Novozymes claims that the patent infringement has caused the firm problems.
"Its very satisfactory that the court agreed that our patent is valid and has been infringed, considering the large amount of resources we use on research, development and patenting," said Novozymes general counsel Kristian Merser.
The case, between Novozymes and Danisco, lasted 1, years and concerned an infringement of one of Novozymes patents on enzymes for bioethanol.
Novozymes claimed in 2004 that Genencor International - later bought by Danisco - was selling enzymes protected by Novozymes patent rights on the booming US ethanol market.
Danisco division Genencor has now voluntarily withdrawn its Spezyme Ethyl product from the market. The company said last week that legal options are currently being reviewed and that appeal of the ruling is being considered.
"Overall, this court ruling will not materially affect Daniscos enzyme business including the ethanol segment," said CEO Tom Knutzen.
"The product withdrawn is just one of a full product range for the ethanol segment, which covers both the traditional ethanol production process and the 'no-cook' process, for which Genencor launched the Stargen 001 product in 2005."
The size of the damages will be decided this autumn. Novozymes has claimed several million US dollars in damages for loss of profits.