The heavy metal thallium is an emerging pollutant among the most potentially toxic species to which human populations are exposed. Its harmful effects on living organisms are well-known at high doses, typical of acute intoxication. Its harmful effects at low doses are by far less known. In a previous paper, we reported a TlCl-induced metabolic shift to lactate and ethanol production in living hippocampal HN9.10e neurons that appeared after a single short exposure (48 h) at low doses (1-100 μg/L). This metabolic shift to lactate and ethanol suggests a marked impairment of cell bioenergetics. In this work, we provide detailed evidence for TlCl-induced changes of neuronal morphology and mitochondrial activity. Confocal microscopy and fluorescent probes were used to qualitatively and quantitatively analyze, at the subcellular level, living HN9.10e neurons during and after TlCl exposure. An early onset mitochondrial dysfunction appeared, associated with signs of cellular deregulation such as neurite shortening, loss of substrate adhesion, and increase of cytoplasmic calcium. The dose-dependent alteration of mitochondrial ROS (mtROS) level and of transmembrane mitochondrial potential (ΔΨm) has been observed also for very low TlCl doses (1 μg/L). The treatment with the ATP synthase inhibitor oligomycin revealed a severe impairment of the mitochondrial function, more significant than that measured by the simple quantification of the tetramethylrhodamine methyl ester (TMRM) fluorescence. These results highlight that mitochondria are a key subcellular target of TlCl neurotoxicity. The transmembrane mitochondrial potential was significantly correlated with the ethanol concentration in cell culture medium ( P < 0.001, r = -0.817), suggesting that ethanol could be potentially used as a biomarker of mitochondrial impairment.