In this article, it is shown that inverse analysis using data assimilation is an indispensable problem-solving methodology for structural health monitoring. Forward and inverse analysis for eddy current testing are considered as sizing estimation of material damages in structured systems. First, testing environments are mathematically described based on a three dimensional eddy current analysis. Secondly, an inversion technique based on Markov Chain Monte Carlo method (MCMC) is employed for solving the crack shape reconstruction. Results on computational experiments are demonstrated in order to show the feasibility and applicability of the proposed method.