In this paper, we discuss how uncertainties can be represented in two of the most well-known multi-criteria decision analysis (MCDA) methods, the multi-attribute utility theory (MAUT) and the analytical hierarchy process (AHP). There are distinct differences in the treatment of uncertainties in the two methods. MAUT is specially developed for handling uncertainties. In contrast, the AHP method has, in its general form, no systematic approach to integrate uncertainty aspects. However, various procedures for applying AHP in situations involving uncertainties have been proposed in the literature. In a case study, we illustrate how the two methods can be used to assist in decision making under uncertainty in a local energy planning problem. We conclude that MAUT is clearly more suited for handling uncertainties than AHP. However, also many other criteria should be considered when choosing which MCDA method to apply for local energy planning purposes