This paper is devoted to discrete choice analysis of behavior of bus and train passengers and their choice between alternative transportation modes. We develop a nested discrete choice model and estimate model parameters on the base of data sample collected in our own survey. We consider Riga-Daugavpils two-way journeys with three possible transportation options a car, a coach, and a train. Using our survey data we analyse factors, which influence passengers choices. A set of factors includes travel specific factors (departure time), factors, which describe passengers age, income, etc. and factors, which describe their behavior (time of arrival to a station before departure). The resulting conclusions of the research have a significant practical utility and have been used to improve operations of Riga International Coach Terminal.