Atypical teratoid/rhabdoid tumours (ATRTs) are among the most-common brain tumours in infants. The prognosis of these patients is predominantly poor, with some exceptions, suggesting the presence of clinically relevant intertumour heterogeneity. Following genetic analysis of 192 ATRTs, researchers were able to assign these tumours to one of three subgroups with largely homogeneous genomes: ATRT-TYR, ATRT-SHH and ATRT-MYC. However, analysis of genome-wide methylation patterns revealed substantial DNA hypermethylation among the ATRT-TYR and ATRT-SHH subtypes, but not the ATRT-MYC subgroup, which is likely to have functional consequences for the expression of tumour suppressors, or oncogenes. Thus, epigenetic analyses might guide the optimal treatment of patients with ATRTs.