Geological heterogeneity 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 the Factor of Safety (FS) for a slope induced by the geological heterogeneity is not well studied in the past. This paper presents a way to evaluate the uncertainty in the FS for a slope in the presence of geological heterogeneity using borehole data. The geological heterogeneity is simulated by an efficient Coupled Markov Chain (CMC) model. Monte Carlo simulation of slope stability is conducted based on the simulated heterogeneous soils. Effect of borehole layout schemes on uncertainty evaluation of FS is investigated. The results show that borehole beyond the influence zone of the slope is not very useful for the evaluation of slope stability. Borehole at the middle part of the slope is essential for a precise evaluation of FS statistics.