The Munich, Germany-based office said it had revised the patent it granted to Edinburgh University, Scotland, in December 1999 on altering animal cells after objections from 14 parties, Reuters reported.
The patent office said officials had not noticed a reference to human cells in the original 235-page application document.
"The much-discussed 'Edinburgh' patent is to be maintained in an amended form, so that it no longer includes human or animal embryonic stem cells," the European Patent Office (EPO) said in a statement after three days of hearings.
The patent breached a European Patent Convention barring use of human embryos for commercial purposes, the EPO said. The subject-matter of the original patent had also never included the cloning of humans or animals.
Greenpeace welcomed the ruling saying it should strike out all patent claims related to human embryos, although it called for clearer guidelines from the European Union.
The EPO covers 24 European countries, including all 15 of the European Union, although it is not an EU institution.
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