In timber structures, the connections are generally flexible in comparison to the members they connect, and so contribute significantly to the dynamic properties of the structure. It is shown here that a widely-used form of connection, the dowel-type connection, exhibits nonlinear stiffness and energy dissipation, even at pre-yield loads, and that this nonlinearity affects the modal properties of structures with such connections. This study investigates that behaviour by modal analysis of a portal frame and a cantilever beam constructed from timber with steel dowel connections. The observed nonlinearity is explained qualitatively by considering the measured force-displacement response of individual connectors under cyclic load, which show a reduction in stiffness and an increase in energy dissipation with increasing amplitude of vibration. The structures were tested by modal analysis under slow sine sweep and pseudo-random excitation. Under pseudo-random excitation, a linear single degree-of-freedom curve fit was applied to estimate the equivalent linear modal properties for a given amplitude of applied force. Under slow sine sweep excitation, the frequency response function for the structures was observed to show features similar to a system with a cubic component of stiffness, and the modal properties of the structures were extracted using the equation of motion of such a system. The consequences for structural design and testing are that two key design parameters, natural frequency and damping, vary depending on the magnitude of vibration, and that parameters measured during in-situ testing of structures may be inaccurate for substantially different loads.