Geological uncertainty appears in the form of one soil layer embedded in another or the inclusion of pockets of different soil type within a more uniform soil mass. Uncertainty in factor of safety (FS) and probability of failure (Pf) of slope induced by the geological uncertainty is not well studied in the past. This paper presents one approach to evaluate the uncertainty in FS and Pf of slope in the presence of geological uncertainty using borehole data. The geological uncertainty is simulated by an efficient coupled Markov chain (CMC) model. Slope stability analysis is then conducted based on the simulated heterogeneous soils. Effect of borehole layout schemes on uncertainty evaluation of FS and Pf is investigated. The results show that borehole within influence zone of the slope is essential for a precise evaluation of FS statistics and Pf. The mean of FS will converge to the correct answer as the borehole number increases.