Transgenes, especially those driving production of the GAL4 transcription factor in a specific spatial pattern, are a critical and widely used tool in the Drosophila research community. We recently noticed loss of GAL4-driven reporter gene expression in a series of crosses, and traced that loss of reporter gene expression to stochastic physical loss of the GAL4 gene in the driver line. We have demonstrated that the instability of the GAL4 transgene can be "cured" by treatment of the line with tetracycline, suggesting that the causative agent is of bacterial origin. A PCR assay revealed that the line is not infected by Wolbachia, an intracellular parasite known to infect a large percentage of stocks in the public stock centers and to affect mutant phenotypes. Our data indicate that other tetracycline-sensitive agents can cause genetic instability of transgenes, and also provides a potential solution to the problem.