The behavior of Bose-Einstein condensates (BEC) with a vortex lattice in a rotating anisotropic trap was studied. The single-particle wave functions for a rotating anisotropy trap were found by exactly diagonalizing the Hamiltonian. The wave functions in the lowest Landau level (LLL) were shown to be written as simple analytic functions in the small anisotropy limit. The results show that the regularity of the vortex configurations observed in an axisymmetric trap is disturbed by the anisotropy of the confinement.