Most reliability analyses of geotechnical structures considering soil heterogeneity mainly focus on inherent variability, namely the heterogeneity in soil parameters. Another type of soil heterogeneity, i.e. geological uncertainty, is not well studied. The geological uncertainty is very common in reality. It appears in the form of one soil layer embedded in another or the inclusion of pockets of different soil types within a more uniform soil mass. Hence, a borehole-based method is proposed to evaluate the uncertainty in probability of failure (Pf) and statistics of factor of safety (FS) for a slope when geological uncertainty is considered. Firstly, different borehole layout schemes are designed using available borehole data. A coupled Markov chain model is constructed to simulate the geological uncertainty. Secondly, slope stability analyses are conducted using a finite element - strength reduction method. Finally, the effect of borehole layout scheme on the uncertainty in FS and Pf of a slope is analyzed. The borehole data in Perth, Australia are adopted to illustrate the effectiveness of the proposed method. The results show that the borehole layout scheme has a significant influence on the uncertainty of FS and Pf of the slope. The FS of the slope in the presence of the geological uncertainty can be described by a Johnson distribution. The Pf and statistics of FS do not necessarily vary with the number of boreholes monotonously. The boreholes within the influence zone of slope are the most effective in evaluating the uncertainty in the FS. The mean of the FS converges to an accurate value as the borehole number increases.