The paper presents the application of Monte Carlo simulation in the behavior analysis of an autonomous underwater vehicle. Due to the highly nonlinear dynamics and existence of uncertain parameters in the models, there is not a straightforward method to analyze the behavior of an autonomous underwater vehicle. The objective of this article is to introduce a Monte Carlo campaign for an autonomous underwater vehicle 6-degree-of-freedom model to examine the effects of uncertain parameters on the mission objectives. Uncertainties in the model are considered in several categories, consisting of hydrodynamic and added mass coefficients, control instruments (sensors and actuators), environmental conditions and initial conditions. Monte Carlo simulations are run for a typical autonomous underwater vehicle moving from the water surface to reach a predetermined depth and heading during the mission time. For this purpose, 6-degree-of-freedom software is developed in C++ which is a fast and visual programming software. Using an example, it is shown that simulation results can be used for tuning of guidance algorithm. Moreover, the proposed concept is applicable for analysis of other types of autonomous ocean systems.