Assessment of methylation state of DNA extracted from brain is becoming one of the most investigated issues in the study of epigenetics and psychopathology. pH effects in brain are known to affect gene transcription, though pH effects on DNA methylation state are unknown. We demonstrate in vitro using an artificially methylated plasmid that DNA methylation state remains stable, even under extreme pH conditions. Next, using two different genomic regions from human DNA, we assess methylation state from both cortical and sub-cortical brain regions using subjects with varying pH levels. No correlation was found between DNA methylation state and pH. These results suggest that DNA methylation state is stable in post-mortem brain.