As in any engineering application, the problem of structural assessment should face the different uncertainties present in real world. The main source of uncertainty in Health Monitoring System (HMS) applications are those related to the sensor accuracy, the theoretical models and the variability in structural parameters and applied loads. In present work, two methodologies have been developed to deal with these uncertainties in order to adopt reliable decisions related to the presence of damage. A simple example, a steel beam analysis, is considered in order to establish a liable comparison between them. Also, such methodologies are used with a developed structural assessment algorithm that consists in a direct and consistent comparison between sensor data and numerical model results, both affected by uncertainty. Such algorithm is applied to a simple concrete laboratory beam, tested till rupture, to show it feasibility and operational process. From these applications several conclusions are derived with a high value, regarding the final objective of the work, which is the implementation of this algorithm within a HMS, developed and applied into a prototype structure.