Method of aligning hardpoints in aeronautical structures comprising the placement of an aeronautical structure which already has at least two hardpoints on an auxiliary structure, where said auxiliary structure in turn comprises a set of positioning elements which allow varying their position according to at least one degree of freedom, wherein it comprises the steps of: a) Installing on the auxiliary structure a laser collimator on an adjustable support which can be adjusted in at least two directions in space for the purpose of orienting the laser beam so that it passes through a number of through holes with which the already installed hardpoints are equipped; b) Coupling translucent coaxiality sensors both in the holes with which the already installed hardpoints are equipped and in through holes with which the positioning elements are also equipped; c) Measuring the deviation of the point where the laser beam strikes the coaxiality sensors located in the hardpoints and in the positioning elements by obtaining its deviation with respect to a local reference system of said coaxiality sensors; d) Once the deviations with respect to the laser beam obtained in the preceding step are known, applying a correction algorithm to calculate the necessary displacements to which the positioning elements are to be subjected for proper alignment of the hardpoints; e) Shifting the positioning elements according to the value obtained in the preceding step, resulting in the positioning element being aligned; f) Taking a new reading of the position of the positioning elements according to paragraph c) above, and in the event of being considered unsuitable according to a previously established quality criterion, performing another calculation of the displacement of the positioning elements by repeating steps d) and e); g) Once it has been found that the alignment between hardpoints and positioning elements is sufficient according to the established quality criterion, locking the position of the positioning elements; and h) Assembling the rest of the hardpoints to then also apply to same the preceding steps b) to g) of the described method. a) Installing on the auxiliary structure a laser collimator on an adjustable support which can be adjusted in at least two directions in space for the purpose of orienting the laser beam so that it passes through a number of through holes with which the already installed hardpoints are equipped; b) Coupling translucent coaxiality sensors both in the holes with which the already installed hardpoints are equipped and in through holes with which the positioning elements are also equipped; c) Measuring the deviation of the point where the laser beam strikes the coaxiality sensors located in the hardpoints and in the positioning elements by obtaining its deviation with respect to a local reference system of said coaxiality sensors; d) Once the deviations with respect to the laser beam obtained in the preceding step are known, applying a correction algorithm to calculate the necessary displacements to which the positioning elements are to be subjected for proper alignment of the hardpoints; e) Shifting the positioning elements according to the value obtained in the preceding step, resulting in the positioning element being aligned; f) Taking a new reading of the position of the positioning elements according to paragraph c) above, and in the event of being considered unsuitable according to a previously established quality criterion, performing another calculation of the displacement of the positioning elements by repeating steps d) and e); g) Once it has been found that the alignment between hardpoints and positioning elements is sufficient according to the established quality criterion, locking the position of the positioning elements; and h) Assembling the rest of the hardpoints to then also apply to same the preceding steps b) to g) of the described method.