In this study, probabilistic analysis of seepage through a two-layered soil foundation was performed. The hydraulic conductivity of soil shows significant spatial variations in different layers because of stratification; further, it varies on a smaller scale within each individual layer. Therefore, the deterministic seepage analysis method was extended to develop a probabilistic approach that accounts for the uncertainties and spatial variation of the hydraulic conductivity in a layered soil profile. Two-dimensional random fields were generated on the basis of the Karhunen-Lo$grave{e}$ve expansion in a manner consistent with a specified marginal distribution function and an autocorrelation function for each layer. A Monte Carlo simulation was then used to determine the statistical response based on the random fields. A series of analyses were performed to verify the application potential of the proposed method and to study the effects of uncertainty due to the spatial heterogeneity on the seepage behavior of two-layered soil foundation beneath water retaining structure. The results showed that the probabilistic framework can be used to efficiently consider the various flow patterns caused by the spatial variability of the hydraulic conductivity in seepage assessment for a layered soil foundation.