The use of antibiotics has recently risen to prominence in neuroscience due to their potential value in studying the microbiota-gut-brain axis. In this context they have been largely employed to illustrate the many influences of the gut microbiota on brain function and behaviour. Much of this research is bolstered by the abnormal behaviour seen in germ-free animals and other well-controlled experiments. However, this literature has largely failed to consider the neuroactive potential of antibiotics themselves, independent from, or in addition to, their microbicidal effects. This is problematic, as clinical as well as experimental literature, largely neglected through the past decade, has clearly demonstrated that broad classes of antibiotics are neuroactive or neurotoxic. This is true even for some antibiotics that are widely regarded as not absorbed in the intestinal tract, and is especially concerning when considering the highly-concentrated and widely-ranging doses that have been used. In this review we will critically survey the clinical and experimental evidence that antibiotics may influence a variety of nervous system functions, from the enteric nervous system through to the brain and resultant behaviour. We will discuss substantial evidence which clearly suggests neuro-activity or -toxicity by most classes of antibiotics. We will conclude that, while evidence for the microbiota-gut-brain axis remains strong, clinical and experimental studies which employ antibiotics to probe it must consider this potential confound.