In this work, routing and spectrum allocation (RSA) algorithms together with network coding (NC) are proposed for elastic optical networks. NC has been used in optical networks for protection against link failures and also in multicasting to improve spectral efficiency. In this work, NC is used to protect confidential connections against eavesdropping attacks. The confidential signals are XOR-ed with other signals at different nodes in their path while transmitted through the network. These signals can be combined either at the source node and/or at intermediate nodes. To implement NC for confidential connections, a set of constraints for the NC problem in addition to the constraints of the RSA problem are incorporated to the algorithms. The combination of signals through network coding significantly increases the security of confidential connections, since an eavesdropper will receive a combination of signals from different connections, making it extremely difficult for the confidential signal to be decrypted. A number of RSA strategies are examined in terms of confidentiality, spectrum utilization, and blocking probability. Performance results demonstrate that network coding provides an additional layer of security for confidential connections with only a small increase in the spectrum usage.