Kant speaks repeatedly about the relations between ends or aims and scientific research, but the topic has mostly been ignored. What is the role of ends, especially (though not exclusively) practical ones, in his views on science? I will show that while Kant leaves ample space for recognizing a function of ends both in the definition and the pursuit of inquiry, and in the further practical application of scientific cognition, he does not claim that science is simply an instrument for achieving practical ends. I explain his complex conception, pointing out that Kant argues (1) that the sciences require ends for their very definition, (2) that ends come in fundamentally different kinds, (3) that the relation between science and ends requires the rational determination and hierarchization of all our ends, with “wisdom” as the highest, and (4) that this determination and hierarchization – which ought to be done by metaphysics – has itself to be carried out in a “scientific way”. I show further that (5) Kant gives sui generis weight to the epistemic aims and standards of science and to the autonomy of science from our practical lives. This places his position between separatism and anti-separatism with regard to the relation between science and our ends or values.