This paper presents the design, development and testing of a low-cost Structural Health Monitoring (SHM) system based on MEMS (Micro Electro-Mechanical Systems) triaxial accelerometers. A new control system composed by a myRIO platform, managed by specific LabVIEW software, has been developed. The LabVIEW software also computes the frequency response functions for the subsequent modal analysis. The proposed SHM system was validated by comparing the data measured by this set-up with a conventional SHM system based on piezoelectric accelerometers. After carrying out some validation tests, a high correlation can be appreciated in the behavior of both systems, being possible to conclude that the proposed system is sufficiently accurate and sensitive for operative purposes, apart from being significantly more affordable than the traditional one.