Monoaminergic challenge tests allow investigating central nervous changes in humans under acute depletion of specific neurotransmitters (5-HT, DA, NE). Along with studies using alpha-methyl-para-tyrosine test (AMPT) and phenylalanine/tyrosine depletion test (APTD), the tryptophan depletion test (ATDT) represents the currently most established human challenge tool for the assessment of brain serotonin functioning. Neurophysiological studies in healthy and clinical samples may contribute to the search for a non-invasive and reliable biological marker of monoaminergic vulnerability or dysfunction. In the design of these studies, various biochemical and methodological aspects have to be taken into account. This article focuses on electrophysiological methodology and results of monoamine depletion studies (i.e., electroencephalography, magnetoencephalography, polysomnography, auditory evoked potentials and startle response).