The discrete orthogonality relations hold for all the orthogonal polynomials obeying three term recurrence relations. We show that they also hold for multi-indexed Laguerre and Jacobi polynomials, which are new orthogonal polynomials obtained by deforming these classical orthogonal polynomials. The discrete orthogonality relations could be considered as more encompassing characterisation of orthogonal polynomials than the three term recurrence relations. As the multi-indexed orthogonal polynomials start at a positive degree $ell_{mathcal D}ge1$, the three term recurrence relations are broken. The extra $ell_{mathcal D}$ `lower degree polynomials, which are necessary for the discrete orthogonality relations, are identified. The corresponding Christoffel numbers are determined. The main results are obtained by the blow-up analysis of the second order differential operators governing the multi-indexed orthogonal polynomials around the zeros of these polynomials at a degree $mathcal{N}$. The discrete orthogonality relations are shown to hold for another group of `new orthogonal polynomials called Krein-Adler polynomials based on the Hermite, Laguerre and Jacobi polynomials.
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