We used microarray analysis to screen the Drosophila genome for effects of Wolbachia infection on transcript levels in wildtype adult immature ovaries. Keywords: Comparative expression analysis of infection effect To generate the ovaries to be compared, we first rid a wildtype Canton-S line of Drosophila of the well characterized YW strain of Wolbachia that it harbored (Bourtzis et al., 1998, Presgraves, 2000) by raising the flies for three generations on food containing tetracycline. After the line had been raised for three more generations on food without tetracycline, we used a standard PCR assay (O'Neil et al., 1999) to confirm that the line was Wolbachia free. Genetically matched infected and uninfected females were recovered as the daughters from two reciprocal crosses between the infected and the cured Canton-S lines. Previtellogenic ovaries were harvested from these females 1-5 h after eclosion