Neural regulation of stress responses, and the feedback of stress hormones to the brain, reflect complex brain-body interactions that may underlie the effects of psychological stress on health. Elucidating the brain circuitry involved in the cortical control of limbic-hypothalamic-pituitary-adrenal axis, and the cortical "targets" of cortisol that in turn modulates brain function, requires careful assessment of glucocorticoid hormones, in the context of the neuroimaging paradigms. Here we discuss approaches for assessment of endocrine function in the context of neuroimaging, including methods of blood and saliva specimen collection, and methods for drug/hormone administration. We also briefly discuss important temporal considerations, including appropriate timing of sample collections for hormones with different time-courses of activation (e.g. ACTH vs. cortisol), the pharmacokinetics of both endogenous hormones and administered agents, and circadian considerations. These are crucial to experimental designs of rhythmic hormonal systems and multiple feedback loops. We briefly address psychological/behavioral 'activation' paradigms used for inducing endogenous LHPA axis responses within or in proximity to scanner, as well as strategies for administration of exogenous hormones or secretagogues. Finally, we discuss some of the analytical issues in terms of hormone responses (e.g. response and area under curve, diurnal variability) and strategies for linking measured levels of peripheral humoral factor to brain activity (e.g. hormone responses as between-subject regressors of BOLD activations, hormone levels as within-subject regressors in analyses of covariance of brain activity over time, etc.).