Multiple choice questions (MCQs) that can be generated from a domain ontology can significantly reduce human effort & time required for authoring & administering assessments in an e-Learning environment. Even though here are various methods for generating MCQs from ontologies, methods for determining the difficulty-levels of such MCQs are less explored. In this paper, we study various aspects and factors that are involved in determining the difficulty-score of an MCQ, and propose an ontology-based model for the prediction. This model characterizes the difficulty values associated with the stem and choice set of the MCQs, and describes a measure which combines both the scores. Further more, the notion of assigning difficultly-scores based on the skill level of the test taker is utilized for predicating difficulty-score of a stem. We studied the effectiveness of the predicted difficulty-scores with the help of a psychometric model from the Item Response Theory, by involving real-students and domain experts. Our results show that, the predicated difficulty-levels of the MCQs are having high correlation with their actual difficulty-levels.