As congestion results not only in the dispersion of origin-destination (O-D) demand across multiple routes but also in peak spreading, use of dynamic traffic assignment models as a means of predicting the impact of a new infrastructure should take into account departure time choice in addition to route choice. Departure time choice may be modeled simultaneously with route choice. In such a model, each traveler has a preferred departure and arrival time, deviation from which results in a certain disutility. Departure time choice can be viewed as route choice in a suitably defined hypernetwork. The combination of departure time choice and route choice in a single framework is called the dynamic user optimum departure time and route choice (DUO-D&R) assignment. When the DUO assignment needs a dynamic O-D matrix with fixed departure times, the DUO-D&R assignment needs a dynamic O-D matrix with preferred departure times. This matrix is called the preferred departure time O-D (pOD) matrix. A method is proposed for estimating the pOD demand matrix that reflects preferred instead of realized departure times. To carry out this estimation, the DUO-D&R problem is formulated and solved. The schedule delay function and the departure choice model are assumed to be known. The possible advantage of the DUO-D&R assignment over DUO assignment is demonstrated through numerical experiments that correspond to scenarios in which infrastructure is expanded and travel demand is subject to uniform growth.