The contingent valuation method was used to elicit Japanese consumers’ willingness-to-pay for genetically modified organism (GMO) segregation programs. The results revealed that most consumers pay nonnegligible premiums for products produced under strict GMO-segregation programs. However, we found that the premium did not vary by the threshold level of GMO content in the product. We further found that a government certification did not increase the premium for GMO-segregation programs. Therefore, an additional mandatory regulation to reduce GMO contaminations would not be worthwhile because such a regulation would incur substantial enforcement costs.