Consumption of alcohol and nicotine results in neurological alterations that may promote continued use of both drugs (Doyon et al., 2013). These alterations are grounded in circuit level changes that can be evaluated through functional connectivity (FC) among specific brain regions (Sutherland et al., 2012). FC studies have found relationships between the intake of alcohol and cognitive, motor and coordination dysregulations (Camchong et al., 2013; Chanraud et al., 2011). Other studies suggest a link between brain FC and motor, attention and memory enhancement due to nicotine administration (Jasinska et al., 2013). In light of these advances, patterns of brain connectivity in alcohol and nicotine users have begun to be investigated as possible diagnostic biomarkers (Camchong et al., 2012; Pariyadath et al., 2014). Understanding how these drugs induce changes in the FC of the brain might be critical for the development of addiction treatment and the improvement of clinical outcomes.