Professor Alessandro Strumia from the University of Pisa, who had been a guest professor at CERN, made the comments during a workshop in September on high-energy theory and gender.
CERN had initially suspended Strumia but said Thursday that it had decided to permanently end the partnership.
"As a result of its own investigation... CERN decided not to extend Professor Strumia's status of Guest Professor," the lab said in a statement.
CERN also noted a public reprimand issued against Strumia by the University of Pisa in January.
Strumia's presentation — which included various slides, charts and graphs — appeared to claim that men face discrimination in the field of physics.
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One pictorial series suggested that women line up to take gender studies and then later protest over a lack of jobs in stem fields, an umbrella term that covers areas like chemistry and engineering.
"Physics invented and built by men, it's not by invitation," one slide said.
CERN, the French acronym for the European Centre for Nuclear Research, is for the first time being led by a female director general: Fabiola Gianotti, an Italian expert in experimental particle physics, took charge in 2016.
The lab has launched a number of initiatives to boost female participation in the sciences, but has conceded that it is far from having achieved gender parity among its staff.
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