Assessment of the stiffness of joints is important for the joints’ design, monitoring the condition of building structures and prognosis of the lifetime and safety of buildings or its elements. Typically, such assessment is done in a non-destructive way using either shock or vibration analysis with a network of accelerometers as sensors. To improve the quality of diagnostics of structural joints and make it more specific, a method and measurement system implementing the principle of correlation of normalized coaxial accelerations measured in 3D space was proposed. The method is based on the mathematical analysis of vibrations of structural joints in 3 spatial directions using 3D accelerometers located at different parts of a joint and orientated coaxially. The correlation method was verified in a laboratory experiment using rigid, semi-rigid and pinned joints of timber beams. Stand with timber beams joined at right angles by steel plates and screws were fabricated and tested by static loading to confirm the present state of the joint. Timber beams with 150X50 mm solid sections made C18 strength class were used for the timber stand. The decrease of the joint’s stiffness in the case of probable damages was modelled by the loosening of the steel screws. The stand was subjected to a vibration load provided by electrodynamics actuators fixed on one of the joint elements. This element was excited by a chirp signal in a frequency sweep range from 10 to 500 Hz, where the most prominent resonance of the stand was found. Acceleration responses were recorded by 3D accelerators placed on the loaded and connected beams. Peak values of the cross-correlation function between the responses from the correspondingly orientated pairs of coaxial accelerometers were determined. It was shown that the difference between the peak values of the correlation functions obtained for the rigid, semi-rigid and hinge joints enabled specification of the joints’ stiffness.