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This paper describes a Markov chain Monte Carlo (MCMC) sampling approach for the estimation of not only the radio refractivity profiles from radar clutter but also the uncertainties in these estimates. This is done by treating the refractivity from clutter (RFC) problem in a Bayesian framework. It uses unbiased MCMC sampling techniques, such as Metropolis and Gibbs sampling algorithms, to gather more accurate information about the uncertainties. Application of these sampling techniques using an electromagnetic split-step fast Fourier transform parabolic equation propagation model within a Bayesian inversion framework can provide accurate posterior probability distributions of the estimated refractivity parameters. Then these distributions can be used to estimate the uncertainties in the parameters of interest. Two different MCMC samplers (Metropolis and Gibbs) are analyzed and the results compared not only with the exhaustive search results but also with the genetic algorithm results and helicopter refractivity profile measurements. Although it is slower than global optimizers, the probability densities obtained by this method are closer to the true distributions.