Two doctors, Dutch and Belgian nationals, were abducted on Sunday on a road between the cities of Rabdhore and Hudur in central Somalia's Bakool region.
"The two expat doctors were taken and all their Somali colleagues were allowed to go," the organization said in a statement. MSF also said the abductors did not use violence, although there had been "some shooting in the air."
Three cars were also taken, but were later found abandoned. The organization has so far failed to establish contact with the doctors or their abductors.
"MSF is doing all that it can to ensure the swift and safe return of our colleagues," the group said.
The aid group, which is the main provider of free healthcare in nine regions of central and southern Somalia, currently has no international staff permanently based in the country. The work is carried out mostly by national staff members, who are assisted whenever possible by an international management team based in Nairobi.