We argue that in large classes of string compactifications with a MSSM-like structure substantial flavor violating SUSY-breaking soft terms are generically induced. We specify to the case of flavor dependent soft-terms in type IIB/F-theory SU(5) unified models, although our results can be easily extended to other settings. The Standard Model (SM) degrees of freedom reside in a local system of 7-branes wrapping a 4-fold S in the extra dimensions. It is known that in the presence of closed string 3-form fluxes SUSY-breaking terms are typically generated. We explore the generation dependence of these soft terms and find that non-universalities arise whenever the flux varies over the 4-fold S. These non-universalities are parametrically suppressed by (M_{GUT}/M_{Pl})^{1/3}. They also arise in the case of varying open string fluxes, in this case parametrically suppressed by alpha_{GUT}^{1/2}. For a standard unification scheme with M_{GUT} = 10^{16} GeV and alpha_{rm GUT} = 1/24 these suppressions are very mild. Although limits from the kaon mass difference Delta m_K are easily obeyed for squark masses above the present LHC limits, constraints from the CP-violation parameter epsilon_K imply squark masses in the multi-TeV region. The constraints from BR(mu rightarrow egamma) turn out to be the strongest ones, with slepton masses of order ~10 TeV or heavier required to obey the experimental limits. These sfermion masses are consistent with the observed large value m_H ~ 126 GeV of the Higgs mass. We discuss under what conditions such strong limits may be relaxed allowing for SUSY particle production at LHC.
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