Studies of comorbid (syntropic) and inversely comorbid (rarely occurring together, i.e., dystropic) diseases have focused on the search for molecular causes of this phenomenon. We investigated DNA methylation levels in regulatory regions of 23 apoptosis-associated genes as candidate loci associated with the "cancer-neurodegeneration" dystropy in patients with Huntington's disease (HD) and patients with non-small cell lung cancer (LC). Statistically significant differences in methylation levels between the HD and LC groups were found for 41 CpG sites in 16 genes. The results show that five genes (, , , , and ) are probably involved in the phenomenon of inverse comorbidity of these diseases. For these genes, the methylation levels of the studied CpG sites were altered in opposite directions in the two groups of patients, compared to the control group. For the gene, the above hypothesis is supported by our analysis of open-access data on gene expression in patients with the aforementioned diagnoses and fits a probable mechanism of the "HD-LC" dystropy.