Biological factors and mechanisms that drive higher prevalence of insomnia in females are poorlyunderstood. This study focused on the neurological consequences of X-chromosome functional imbalancesbetween sexes. Benefited from publicly available large-scale genetic, transcriptional and epigenomic data, we curated andcontrasted different gene lists: (1) X-liked genes, including assignments for X-chromosome inactivation patterns anddisease associations; (2) sleep-associated genes; (3) gene expression markers for the suprachiasmatic nucleus. We show that X-linked markers for the suprachiasmatic nucleus are significantly enriched for clinicallyrelevant genes in the context of rare genetic syndromes and brain waves modulation. Considering female-specific patterns on brain transcriptional programs becomes essential whendesigning health care strategies for mental and sleep illnesses with sex bias in prevalence.