Public concern for the humane treatment of animals in research has led to specific guidelines for appropriate treatment of study organisms. Field research poses special challenges that Institutional Animal Care and Use Committees find difficult to address based on existing guidelines. Toe clipping is a common but contentious example whose use has been called barbaric and whose efficacy has been questioned. We provide a brief review of the ethical bases for such positions, the legal framework they have engendered, and the scientific evidence regarding the impacts of the practice. Leading philosophical views vary but tend to focus on the suffering or distress of individual animals, primarily vertebrates. The law has adopted this individual-centered view. Biologists, in contrast, tend to more wholistic views that focus on populations and ecosystems. Scientific studies of the impacts of toe clipping, most of them relatively recent, have become increasingly sophisticated statistically. Most show little impact of toe clipping on study animals, the exception being the likelihood of recapture of toe-clipped individuals in some frogs. If unaccounted for, effects of methodology can bias scientific findings. The few studies focusing on physiological indicators of distress show no increase resulting from toe-clipping. Thus, toe clipping of reptiles and amphibians meets legal and ethical expectations and should remain acceptable where it meets study needs. Biologists have long been concerned about the possible ethical implications of their methods. Philosophical inquiry has been beneficial in improving our understanding of these methods, but the need of biologists for better philosophical elaboration of ecological ethics has only partially been addressed.