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The zero modes of the non-relativistic vortices are examined by index calculation for the self-dual equations. The index for the self-dual equations is zero for non-Abelian groups, but a non-zero index is obtained by the Toda Ansatz which reduces the self- dual equations to the Toda equations. The number of zero modes for the non-relativistic Toda vortices is \\(2\\sum^{r}_{\\alpha,\\beta}K_{\\alpha \\beta}Q^{\\beta}\\) which is twice the total number of isolated zeroes of the vortex functions. For the affine Toda system, there are additional adjoint zero modes which give a zero index for the SU(N) 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