Three-dimensional linear spin-wave eigenmodes of a vortex-state Permalloy disk are studied by micromagnetic simulations based on the Landau-Lifshitz-Gilbert equation. The simulations confirm that the increase of the disk thickness leads to the appearance of additional exchange-dominated so-called gyrotropic flexure modes having nodes along the disk thickness, and eigenfrequencies that decrease when the thickness is increased. We observe the formation of a gap in the mode spectrum caused by the hybridization of the first flexure mode with one of the azimuthal spin-wave modes of the disk. A qualitative change of the transverse profile of this azimuthal mode is found, demonstrating that in a thick vortex-state disk the influence of the "transverse" and the "azimuthal" coordinates cannot be separated. The threedimensional character of the eigenmodes is essential to explain the recently observed asymmetries in an experimentally obtained phase diagram of vortex-core reversal in relatively thick Permalloy disks. DOI: 10.1103/PhysRevLett.117.037208 The study of spin-wave (SW) excitations in micro-and nanosized magnetic elements is one of the most important topics in modern magnetism. The dynamic spin-wave eigenmodes of finite-size magnetic elements not only determine the high-frequency properties of these elements, but also provide valuable information about remagnetization processes in nanomagnetic objects, as the change of the magnetic ground state of an element is, usually, happening through the softening of one of the SW eigenmodes of this element. When the ground state of magnetization in a magnetic element is spatially uniform the spatial distribution of the spin-wave excitations can, usually, be factorized, and represented as a product of three functions of three independent coordinates (separation ansatz).The situation becomes much more complicated in the case when the magnetic element is thick, so that it has to be treated as three-dimensional (3D), and the magnetization ground state of the element is spatially nonuniform. In that case the possibilities of traditional analytic methods are limited; however, the essential information about SW excitations can be obtained from micromagnetic simulations. As it will be shown below, in a 3D spatially nonuniform case the dependence of the spin-wave mode profile on some of the spatial coordinates gets mixed, and the above discussed separation ansatz traditionally used in the analytic theory does not work anymore.A relatively simple example of a magnetic element having spatially nonuniform ground state of static magnetization is a vortex-state magnetic disk [1][2][3]. In a cylindrical nanodisk with thickness h of a few tens of nanometers and diameter 2R of typically several hundred nanometers the magnetic ground state is a vortex. There the magnetization curls in the plane of the disk with a clockwise (CW) or counterclockwise (CCW) circulation. At the center of the disk in an area with a typical diameter of 10 to 20 nm the magnetization turns out of the plane [3] form...