We show several arithmetic estimates for Hilbert's Nullstellensatz. This includes an algorithmic procedure computing the polynomials and constants occurring in a Bézout identity, whose complexity is polynomial in the geometric degree of the system. Moreover, we show for the first time height estimates of intrinsic type for the polynomials and constants appearing, again polynomial in the geometric degree and linear in the height of the system. These results are based on a suitable representation of polynomials by straight-line programs and duality techniques using the Trace Formula for Gorenstein algebras. As an application we show more precise upper bounds for the function πS(x) counting the number of primes yielding an inconsistent modular polynomial equation system. We also give a computationally interesting lower bound for the density of small prime numbers of controlled bit length for the reduction to positive characteristic of inconsistent systems. Again, this bound is given in terms of intrinsic parameters.