MSF says that within three hours three hospitals in Damascus that are supported by MSF saw 3,600 patients with neurotoxic symptoms.
MSF's Dr Bart Janssens: "The patients displayed severe symptoms - narrowing of the pupils, breathing difficulties, excessive saliva - which we are linking to neurotoxic chemicals."
The Syrian opposition has blamed the attack on the Assad regime. It speaks of 1,300 casualties.
MSF has not visited the location, but has been in touch with medical staff in the Damascus hospitals. The ngo speaks of a violation of the human rights that ban the use of chemical and biological warfare.
Patients were treated with atropine supplied by MSF. It is a medicine used to combat neurotoxic symptoms.
The Assad regime has meanwhile accused the opposition of using chemical weapons. State TV reported chemical weapons were stockpiled in opposition tunnels in the capital.