DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation. A sequence-capture bisulfite sequencing approach was implemented to monitor context-specific DNA methylation patterns in ~15Mb of the maize genome for a population of plants that had been regenerated from tissue culture. Plants that have been regenerated from tissue culture exhibit gains and losses of DNA methylation at a subset of genomic regions. There was evidence for a high rate of homozygous changes to DNA methylation levels that occur consistently in multiple independent tissue culture lines suggesting the existence of a targeted process for altering epigenetic state during tissue culture. The consistent changes induced by tissue culture include both gains and losses of DNA methylation and can affect CG, CHG or both contexts within a region. The majority of changes in DNA methylation exhibit stable inheritance although there is some evidence for stochastic reacquisition of the initial epigenetic state in some individuals. This study provides insights into the susceptibility of some loci and potential mechanisms that could contribute to altered DNA methylation and epigenetic state that occur during tissue culture in plant species.