Engineered proteins are attractive affinity scaffolds for molecular imaging and drug delivery. Although exquisite binding specificity and affinity can be engineered, many proteins exhibit off-target uptake, particularly in the kidneys and liver, from physiologic effects. We quantified the ability to alter renal and hepatic uptake via hydrophilic and charge mutations. As a model protein, we used the 10th type III domain of human fibronectin, which has been engineered to bind many targets and has been validated for molecular imaging. We screened rational mutants, identified by structural and phylogenetic analyses, to yield eight mutations that collectively substantially increase protein hydrophilicity. Mutation of two parental clones yielded four domains with a range of hydrophilicity. These proteins were labeled with ⁶⁴Cu, injected intravenously into nu/nu mice (n = 3–5 each) and evaluated by positron emission tomography. Renal uptake strongly correlated with hydrophilicity (Pearson's correlation coefficient = 0.97), ranging from 29 ± 11 to 100 ± 22% ID/g at 1 h. Hepatic uptake inversely correlated with hydrophilicity (Pearson's correlation coefficient = −0.92), ranging from 30 ± 7 to 3 ± 1% ID/g. Thus, renal and hepatic uptake are directly tunable through hydrophilic mutation, identifiable by structural and phylogenetic analyses. To investigate charge, we mutated acidic and basic residues in both parental clones and evaluated ⁶⁴Cu-labeled mutants in nu/nu mice (n = 5–7). Selected charge removal reduced kidney signal: 78 ± 13 to 51 ± 8%ID/g (P < 0.0001) for the hydrophilic clone and 32 ± 10 to 21 ± 3 (P = 0.0005) for the hydrophobic clone. Elucidation of hydrophilicity and charge enabled modulation of background signal thereby enhancing the utility of protein scaffolds as translatable targeting agents for molecular imaging and therapy.