  We show how to avoid unnecessary and uncontrolled assumptions usually made in the literature about soft SU(3) flavor symmetry breaking in determining the two-flavor nucleon matrix elements relevant for direct detection of WIMPs. Based on SU(2) Chiral Perturbation Theory, we provide expressions for the proton and neutron scalar couplings $f_u^{p,n}$ and $f_d^{p,n}$ with the pion-nucleon sigma-term as the only free parameter, which should be used in the analysis of direct detection experiments. This approach for the first time allows for an accurate assessment of hadronic uncertainties in spin-independent WIMP-nucleon scattering and for a reliable calculation of isospin-violating effects. We find that the traditional determinations of $f_u^p-f_u^n$ and $f_d^p-f_d^n$ are off by a factor of 2. 
Accurate evaluation of hadronic uncertainties in spin-independent   WIMP-nucleon scattering: Disentangling two- and three-flavor effects