A system for assembling two parts, in particular parts forming the fuselage or the wings of an aircraft, includes a positioning aid guiding positioning tools so as to juxtapose the two parts at the level of an assembly zone. The assembly system further includes a set of eddy current sensors positioned in at least one of the two parts to determine the separation of the two parts at the level of the assembly zone. If the separation does not conform to a predetermined criterion the positioning tools move at least one of the parts.