A system for assembling two parts (A, B), in particular parts forming the fuselage (100) or the wing of an aircraft, comprises positioning assistance means (400) guiding positioning tools so as to juxtapose the two parts (A, B) at an assembly zone (300). The assembly system further comprises a set of eddy current sensors (20) positioned in at least one of the two parts (A, B), to determine the spacing (d) of the two parts (A, B) at the level of the assembly zone (300). If the distance (d) does not comply with a predetermined criterion, the positioning tools move at least one of the parts (A, B)
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