Field endocrinology techniques allow the collection of samples (i.e., blood, urine, feces, tissues) from free-living animals for analysis of hormones, receptors, enzymes, etc. These data reveal mechanisms by which individuals respond to environmental challenges, breed, migrate and regulate all aspects of their life cycles. Field endocrinology techniques can also be used to address many issues in conservation biology. We briefly review past and current ways in which endocrine methods are used to monitor threatened species, identify potential stressors and record responses to environmental disturbance. We then focus on one important aspect of conservation: how free-living populations respond to human disturbance, particularly in relation to ecotourism. Breeding adult Magellanic penguins, Spheniscus magellanicus, appear to habituate well to tourists, and breed in an area where about 70,000 people visit during the season. Baseline levels of corticosterone return to normal after exposure of naïve birds to humans. However, penguin chicks appear to show a heightened adrenocortical response to handling stress in nests exposed to tourists, compared to chicks living in areas isolated from human intrusions. Given that developmental exposure to stress can have profound influences on how individuals cope with stress as adults, this potential effect of tourists on chicks could have long-term consequences. This field endocrine approach identified a stressor not observed through monitoring behavior alone.