Epigenetic modifications, such as DNA methylation, are understood as an intermediary between environmental factors affecting disease risk and pathophysiologic changes to brain structure and function. Cerebral monoamine oxidase A (MAO-A) levels are altered in depression, as are DNA methylation levels within the MAOA gene, particularly in the promoter / exon I / intron I region. An effect of MAOA methylation on peripheral protein expression was shown, but the extent to which methylation affects brain MAO-A levels is not fully understood. Here, the influence of average and CpG site-specific MAOA promoter / exon I / intron I region DNA methylation on global MAO-A distribution volume (VT), an index of MAO-A density, was assessed via [11C]harmine positron emission tomography in 22 patients suffering from winter-type seasonal affective disorder and 30 healthy controls. No significant influence of MAOA DNA methylation on global MAO-A VT was found, despite correction for health status (patients vs. controls), sex, season (methylation analysis in spring / summer vs. fall / winter) and MAOA variable number of tandem repeat genotype (VNTR; high vs. low expression groups). However, in female subjects, season affected average DNA methylation, with higher levels in spring and summer (puncorr = 0.03). We thus did not find evidence for an effect of MAOA DNA methylation on brain MAO-A VT. In contrast to a previous study that demonstrated an effect of the methylation of a MAOA promoter region located further 5' on brain MAO-A, in the present study MAOA methylation appears to affect brain protein levels to a limited extent. The observed effect of season on methylation levels is in accordance with extensive evidence for seasonal effects within the serotonergic system.