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Accurate and precise characterization of the subsurface stratigraphic configuration (geological model) at a given site is crucial to geotechnical engineering work. The uncertainty in the derived stratigraphic configuration can be significant, due to the strata's complexity and inherent spatial variability coupled with the limited availability of borehole data. The characterization and reduction of this uncertainty should be part of any site characterization project. This paper presents a method for characterization of the subsurface stratigraphic configuration with limited borehole data. Within the framework of the proposed method, the spatial correlation between the existence of a stratum in one subsurface zone and that in the other subsurface zone (or the spatial correlation of the existence of the stratum) is captured by an autocorrelation function determined with the maximum likelihood principle. The initial stratigraphic configurations are first sampled with the conditional random field theory. Next, the maximum-a-posteriori (MAP) estimates of the initial stratigraphic configurations are derived using Markov Chain Monte Carlo (MCMC) and taken as the final stratigraphic realizations. The effectiveness of the proposed method and its advantages over the existing stratigraphic characterization methods are demonstrated through a series of comparative analyses. The versatility of the new approach in modeling the 3-D stratigraphic configuration is further revealed through a case study of a site in Western Australia. This paper adds to the literature on stratigraphic uncertainty characterization and provides a basis for a risk-based geotechnical assessment that considers geological and geotechnical uncertainties. • A probabilistic method for characterizing stratigraphic configuration is proposed. • The spatial correlation of strata is estimated with maximum likelihood principle. • Conditional random field theory and MCMC method are included in this method. • Versatility of this method in modeling 3-D stratigraphic configurations is studied. [ABSTRACT FROM AUTHOR]