  We investigate the implications of non-standard interactions on neutrino
oscillations in the OPERA experiment. In particular, we study the non-standard
interaction parameter $\epsilon_{\mu\tau}$. We show that the OPERA experiment
has a unique opportunity to reduce the allowed region for this parameter
compared with other experiments such as the MINOS experiment, mostly due to the
higher neutrino energies in the CNGS beam compared to the NuMI beam. We find
that OPERA is mainly sensitive to a combination of standard and non-standard
parameters and that a resulting anti-resonance effect could suppress the
expected number of events. Furthermore, we show that running OPERA for five
years each with neutrinos and anti-neutrinos would help in resolving the
degeneracy between the standard parameters and $\epsilon_{\mu\tau}$. This
scenario is significantly better than the scenario with a simple doubling of
the statistics by running with neutrinos for ten years.
