Research in ecology and wildlife biology remains crucial for increasing our knowledge and improving species management and conservation in the midst of the current biodiversity crisis. However, obtaining information on population status often involves invasive sampling of a certain number of individual animals. Marking and sampling practices include taking blood and tissue samples, toe-clipping of amphibians and rodents, or using implants and radio-transmitters – techniques that can negatively affect the animal. Wildlife research may then result in a fundamental conflict between individual animal welfare and the welfare of the population or ecosystem, which could be significantly reduced if non-invasive research practices were more broadly implemented. Implementation of non-invasive methods could be guided by the so-called 3Rs principles for animal research (replace, reduce, refine), which were proposed by Russell and Burch 60 years ago and have become a part of many animal protection legislations worldwide. However, the process of incorporating the 3Rs principles into wildlife research has been unfortunately rather slow and their importance overlooked. In order to help alleviate this situation, here I provide an overview of the most common practices in wildlife research, discuss their potential impact on animal welfare, and present available non-invasive alternatives.