Arctic marine mammals accumulate some of the highest mercury (Hg) levels among all organisms. Despite the fact Hg is a proven neurotoxicant, little is known about its neurotoxic risk to Arctic marine mammals. Here we determined the distribution of Hg (total and organic) in ten brain regions of functional significance (frontal cortex, temporal cortex, occipital cortex, basal ganglia, brain stem, cerebellum, hippocampus, hypothalamus, thalamus, and pituitary) of harbor porpoise (Phocoena phocoena; n=12; Denmark), pilot whale (Globicephala melas; n=6; Faroe Islands), and polar bear (Ursus maritimus; n=37; East Greenland). To explore if brain Hg (total and/or organic) levels are of neurological concern to these marine mammals, we assessed neurochemical enzymes (glutamic acid decarboxylase (GAD), glutamine synthetase (GS)) and receptors (N-methyl-D-aspartic acid (NMDA), GABA(A) (benzodiazepine)) that play critical roles in learning and coordination among the different brain regions. Highest Hg levels were found in the pituitary (mean: 1.6ppm dry weight; range: 0.4–10ppm) of polar bears, pituitary (7.6ppm, 0.55–58 ppm) and frontal cortex (8.2ppm, 0.51–34ppm) of harbor porpoises, and three cortex regions (9.8ppm, 0.17–28ppm) of pilot whales. The brain levels of Hg found in harbor porpoise and pilot whale were comparable to levels that exceed subclinical thresholds in mammalian wildlife. In polar bear, despite relatively low levels, total Hg in only the pituitary was significantly correlated with age categories. Organic Hg comprised about 50% of the total Hg in the pituitary (compared to other brain regions where >80% of total was organic), and this may be of toxicological significance. When brain Hg was related to neurochemical biomarkers, some significant correlations were found. For example, in the harbor porpoise, pituitary Hg and GABA(A) receptor levels (n=8; r=0.923; p<0.01), and frontal cortex Hg and GAD activity (n=5; r=-0.934; p<0.01) significantly correlated. In the polar bear, organic Hg negatively associated with NMDA receptor levels in frontal cortex (n=17; r=-0.545; p<0.05). Overall, these results suggest that certain marine mammals (pilot whales, harbor porpoise) in the Arctic region are exposed to Hg at levels capable of causing subclinical neurological effect, but others (polar bears) may have developed unique schemes to limit brain exposures. Given that Hg is a potent neurotoxicant and that disruptions to neurochemistry precede structural and functional damage to the nervous system, it raises further questions about ecological and physiological impacts of Hg on Artic marine mammals health.