Somatic hypermutation (SHM), class switch recombination (CSR), and gene conversion of immunoglobulin genes require activation-induced cytidine deaminase (AID). AID initiates these events by deaminating cytidines within antibody variable and switch regions. The mechanism that restricts mutation to antibody genes is not known. Although genes other than antibody genes have been found to mutate, not all highly transcribed genes mutate. Thus, somatic hypermutation does not target all genes and suggests a mechanism that either recruits AID to genes for mutation, and/or one that protects genes from promiscuous AID activity. Recent evidence suggests that AID deaminates methyl cytidines inefficiently. Methylation of cytidines could thus represent a means to protect the genome from potentially harmful AID activity that occurs outside of the immunoglobulin loci. To test this premise, we examined whether AID could deaminate methylated-CpG motifs in different sequence contexts. In agreement with a report that suggests that AID has processive-like properties in vitro, we found that AID could completely deaminate single-stranded DNA tracks in plasmid substrates that were greater than 300 nucleotides in length. In addition, methylated-CpG motifs, but not their unmethylated counterparts, were protected from AID-mediated deamination. However, methylation did not protect cytidines that neighbored CpG motifs indicating that methylation per se does not provide a more global safeguard against AID-mediated activity. These data also suggest that AID, and possibly other related cytidine deaminases, might represent a more rapid alternative to bisulfite sequencing for identifying methylated-CpG motifs.