In recent yearsestradiol has emerged as a potential regulator of transient receptor potential vanilloid (TRPV) cationic channels in the peripheral tissues and sensory neurons, however, its analogous role in theCNS is poorly understood. TRPV channels modulate Ca signalling, neurotransmission and behaviour, andexpression of these ion channels and estrogen receptors show a great degree of overlap in different brain regions. Herein, we probe if TRPV1-6 genes contain estrogen receptor-binding sites and if their expression in different brain regions is modulated during estrous cycle. Bioinformatics analysis of the mouse TRPV1-6 gene sequences showed presence of putative functional estrogen response element in their promoter regions. Using qRT-PCR, TRPV1-6 mRNA expression was observed in the olfactory bulb, cortex, hypothalamus, hippocampus, brainstem, and cerebellum of mouse. In these regions, compared to estrus, metestrus, and diestrus, reduced levels of TRPV1 and TRPV5 but elevated TRPV2 and TRPV6 mRNA levels were observed during proestrus. Lower levels of TRPV3 and TRPV4 mRNAs were seen during estrus but higher expression of TRPV3 during metestrus and diestrus, and TRPV4 during proestrus was observed. Estradiol seems to regulate TRPV1/TRPV5 and TRPV2/TRPV6 mRNA expression in opposite manner. Except TRPV4 mRNA expression in the hippocampus and TRPV6 expression in the olfactory bulb, hippocampus and brainstem, expression of other member of TRPV subfamily in distinct brain regions of male mice was comparable to those in metestrus and diestrus mice. We suggest that the circulating levels of estradiol during the estrous cycle may differentially regulate the activity of TRPV1-6 ion channels in the brain.