Changes in genomic methylation patterns are often associated with cancer processes. The development of new, high-throughput techniques for mapping aberrant methylation patterns, along with various forms of DNA damage, will be important for advancing cancer research. Single-molecule real-time (SMRTTM) sequencing yields a rich set of information about nucleic acid structure that allows direct detection of various forms of modified nucleotides, including 5-methylcytosine, 5-hydroxymethylcytosine, N6-methyladenosine, and 8-oxoguanosine. We have studied DNA templates with a range of CpG methylation patterns, and we describe how this approach, in combination with circular consensus sequencing of individual DNA molecules, can be used for base-pair resolution identification of epigenetic modifications. Unlike current bisulfite-sequencing techniques, which are limited by short read lengths and by the reduction in genomic complexity, our method will enable mapping of methylation patterns within even highly repetitive genomic regions. Overall, these results highlight the potential applications of the SMRTTM technology to high-throughput sequencing of methylation and mutagenic DNA lesions. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1154.