The evolution of pest resistance to transgenic crop plants producing insecticidal toxins from Bacillus thuringiensis (Bt) Berliner poses a continuing threat to their sustainable use in agriculture. One component of the U.S.-wide resistance management plan for Bt cotton, Gossypium hirsutum L., involves monitoring the frequency of resistance alleles in field populations. However, existing methods are expensive and may not detect recessive resistance alleles until their frequencies are too high for countermeasures to be effective; therefore, more sensitive methods are needed. The first Bt resistance-causing mutation described at the molecular level was a retrotransposon insertion into the gene encoding a 12-cadherin-domain protein expressed in the midgut of larval Heliothis virescens (F.). We report the first large-scale screen for this mutation using a polymerase chain reaction (PCR)-based approach on >7,000 field-collected individuals. The specific insertion was not detected in any of these samples, nor was it detected in three progeny-tested, field-caught males thought to carry a Bt resistance gene. Unlike the targets of many chemical insecticides where a limited number of resistance-causing mutations compatible with viability can occur; a very large number of such mutations seem possible for the 12-cadherin-domain gene. However, even if these mutations are viable in the laboratory, they may not threaten the effectiveness of transgenic crops because of a high fitness cost in the field. The challenge remains to detect the subset of possible resistance-conferring alleles that are still rare but are viable in the field and increasing due to selection by Bt cotton. This situation will complicate PCR-based Bt resistance monitoring strategies.