Low-Density Parity Check (LDPC) codes and Reed Solomon (RS) codes are two of the most widely used Error Correcting Codes (ECC) for designing of secure biometric systems. In this paper, a performance comparison between LDPC codes and RS codes is proposed in an iris verification system with secure template storage. By analysing the genuine and impostor Hamming distance distributions, resulting from intra- and inter-domain comparisons between the CASIA database iris images, the ECC properties which influence the performance of the system in terms of False Rejection Rate (FRR) and False Acceptance Rate (FAR) are deduced. In this sense, the present work can be considered a useful tool for choosing the most appropriate code for a biometric system with secure template storage.