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In our contribution we continue our discussion with L. Novák, who criticised our paper “Různá pojetí matematiky u vybraných autorů od antiky po raný novověk.” Novák’s critique titled “Tomáš Akvinský instrumentalistou v matematice?” served as an incentive for us not only to clarify certain points, but also to deepen our original exposition. We focused on Aquinas’s understanding of mathematics, the middle sciences and philosophy. We still insist that two substantially different interpretations of these disciplines are possible. On the one hand, there is much evidence for Aquinas’s realistic approach to mathematics and the middle sciences. On the other hand, ideas can also be found in Aquinas’s texts supporting an instrumentalist reading. In our opinion, it is important to point out these two approaches to the mathematical sciences in order to adequately understand the subsequent evolution of the history of ideas, especially in the modern period.