Bisulfite sequencing, a standard method for DNA methylation profile analysis, is widely used in basic and clinical studies. This method is limited, however, by the time-consuming data analysis processes required to obtain accurate DNA methylation profiles from the raw sequence output of the DNA sequencer, and by the fact that quality checking of the results can be influenced by a researcher's bias. We have developed an interactive and easy-to-use web-based tool, QUMA (quantification tool for methylation analysis), for the bisulfite sequencing analysis of CpG methylation. QUMA includes most of the data-processing functions necessary for the analysis of bisulfite sequences. It also provides a platform for consistent quality control of the analysis. The QUMA web server is available at http://quma.cdb.riken.jp/.