Intratumoral heterogeneity plays a critical role in tumor evolution. To define the contribution of DNA methylation to heterogeneity within tumors, we performed genome-scale bisulfite sequencing of 104 primary chronic lymphocytic leukemias (CLLs). Compared with 26 normal B cell samples, CLLs consistently displayed higher intrasample variability of DNA methylation patterns across the genome, which appears to arise from stochastically disordered methylation in malignant cells. Transcriptome analysis of bulk and single CLL cells revealed that methylation disorder was linked to low-level expression. Disordered methylation was further associated with adverse clinical outcome. We therefore propose that disordered methylation plays a similar role to that of genetic instability, enhancing the ability of cancer cells to search for superior evolutionary trajectories. Display omitted •CLL harbors higher intrasample methylation variability compared with normal B cells•Higher intrasample variability arises from stochastically disordered methylation•Methylation disorder is associated with transcriptional variation•Methylation disorder affects genetic evolution and clinical outcome Landau et al. perform bisulfite sequencing of primary chronic lymphocytic leukemias and find high levels of intrasample variability in DNA methylation patterns. Their findings suggest that disordered methylation plays a role similar to that of genetic instability in conferring adaptive advantage to cancer cells.