Transgenic crops expressing Bacillus thuringiensis (Bt) endotoxins have become one of the most important tools for managing co and cotton insect pests in the US and other countries. The widespread adoption of transgenic Bt crops could place a high degree of selection pressure on the target insect populations and accelerate development of resistance, raising conces about the long-term durability of Bt plants as an effective pest management tool. Conservation of Bt susceptibility in insects has become one of the most active research areas in mode agriculture. One of the key factors for a successful Bt resistance management plan is to have a cost-effective monitoring system that can provide information on: (i) the initial Bt resistance allele frequencies at low levels in field insect populations; and (ii) early shifts in Bt resistance allele frequencies so that proactive measures for managing resistance can be deployed well before field control failures. Developing such a monitoring program has been difficult because: (i) resistance traits that occur at very low frequencies are hard to detect; (ii) many factors affect the sensitivity and accuracy of a Bt resistance monitoring program; and (iii) monitoring resistance is costly. Several novel methods for detecting Bt resistance alleles developed during the last decade have made a cost-effective monitoring system possible. Future studies should focus on how to improve and standardize the methodologies for insect sampling and Bt resistance detection.