Multimode polymer waveguides have attracted strong interest for use in high-speed board-level interconnections as they can be cost-effectively integrated onto standard printed circuit boards (PCBs) and flexible substrates using conventional methods of the electronics industry and provide low-loss (<0.04 dB/cm at 850 nm) and high-bandwidth (>30 GHz×m) interconnection. Various high-capacity passive optical backplanes have been demonstrated using this technology while data transmission up to 40 Gb/s using NRZ modulation has been reported. Despite however the intensive research in this technology, very few studies have been reported on mode mixing effects in such multimode waveguides. Mode mixing is a very important phenomenon in highly-multimoded systems as it greatly affects the mode power distribution and therefore, light propagation inside these waveguides. Important transmission characteristics such as their loss and bandwidth performance are affected as well as the behaviour of passive waveguide components such as bends, crossings and couplers due to the different mode distribution at their input. In this work therefore, we present theoretical and experimental studies on mode mixing in polymer multimode waveguides used in board-level optical interconnects. Measurements are carried out on 24-cm long flexible waveguide samples to assess the strength of mode mixing using two common methods used in multimode fibre: mandrel wrapping and micro-bending, while a simple ray tracing model is developed to correlate mode mixing strength with waveguide sidewall roughness. The combination of experimental and theoretical studies can indicate the strength of the effect over the practical range of lengths (∼1 m) which are relevant to the application.