Dozens of armed police, some wearing balaclavas, stood in front of a police van blocking a street in the run-down area of the capital, the site of a number of arrests following the attacks in France which kiled 129 people.
Police issued a warning over a loudspeaker to residents, AFP reporters said, while Belgian media reported that officers had surrounded a house and were telling the occupants to come out.
Belgian prosecutors had no immediate comment on the raid.
Paris attacker Brahim Abdeslam, a Belgium-based Frenchman who blew himself up outside a bar on Boulevard Voltaire, was from Molenbeek.
French police have launched an international manhunt for Abdeslam's Brussels-born brother Salah, who is also said to be linked to the Paris attacks.