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This paper studies the synthesis of controllers for discrete-time, continuous state stochastic systems subject to omega-regular specifications using finite-state abstractions. We present a synthesis algorithm for minimizing or maximizing the probability that a discrete-time stochastic system with finite number of modes satisfies an omega-regular property. Our approach uses a finite-state abstraction of the underlying dynamics in the form of a Bounded-parameter Markov Decision Process (BMDP) arising from a finite partition of the system's domain. Such abstractions allow for a range of transition probabilities between states for each action. Our method analyzes the product between the abstraction and a Deterministic Rabin Automaton encoding the specification. Synthesis is decomposed into a qualitative problem, where the greatest permanent winning components of the product are created, and a quantitative problem, which requires maximizing the probability of reaching this component. We propose a metric for the quality of the controller with respect to the abstracted states and devise a domain partition refinement technique to reach a quality target. Next, we present a method for computing controllers for stochastic systems with a continuous input set. The system is assumed to be affine in input and disturbance, and we derive a technique for solving the qualitative and quantitative problems in the abstractions of such systems called Controlled Interval-valued Markov Chains. The greatest permanent component of such abstractions are found by partitioning the input space to generate a BMDP accounting for all possible qualitative transitions between states. Maximizing the probability of reaching this component is cast as an optimization problem. Quality of the synthesized controller and a refinement scheme are described for this framework.