This document is a thesis submitted by Milan Bouda in partial fulfillment of the requirements for a Doctor of Philosophy degree. The thesis is dedicated to Bayesian estimation of DSGE models. It first outlines the history and development of DSGE modeling in the Czech Republic and worldwide. It then describes the comprehensive DSGE framework and provides details on specifying and estimating DSGE models within this framework. The thesis contains two empirical studies - the first estimates a New Keynesian DSGE model for the Czech Republic using Bayesian techniques, and the second develops a Small Open Economy DSGE model for the Czech Republic with a housing sector.