“God created, Linnaeus organized.” This remark Linnaeus liked to say captures the common idea that the proper task of scientists in classification is to discover and systematize features of the world without being committed to individual perspectives, values, and interests. However, it is rarely the case that scientists passively read nature or carve nature at its joints. My thesis investigates how scientific classification is laden with values and explores its implication. I hope to temper the influence of the ideal of value-free science on the discussion of natural kinds. Contrary to the blossoming scholarship in the values and science literature, there has been little discussion about the role of values in scientific classification. Defined as groupings that correspond to real divisions in nature, natural kinds are considered to exist independently from human values and interests. I demonstrate how the assumptions behind scientific classification endorse the idea of value-free science. Using case studies, I argue that incorporating social, moral, and political values can lead to the epistemic improvement of the category. If values are ineliminable from science, then the question arises, what or whose values, in what ways, can legitimately influence science? I critically examine recently developed criteria for proper uses of values in science. I advocate evaluating values in terms of epistemic benefits. The task of assessing epistemic benefits requires scrutinizing a research program’s social and historical context. Finally, the last part of this dissertation explores how values uniquely influence natural kind terms via social entrenchment. Many philosophers identify projectibility as a defining feature of natural kinds. I look at whether social and cultural practices influence projectibility. I investigate whether these practices affect which kind terms get socially entrenched. I argue that the projectibility of natural kind terms substantially depends on our norms and values.