A novel and quantitative high throughput screening approach was explored as a tool for the identification of novel compounds that inhibit chlamydial growth in mammalian cells. The assay is based on accumulation of a fluorescent marker by intracellular chlamydiae. Its utility was demonstrated by screening 42,000 chemically defined compounds against Chlamydia caviae GPIC. This analysis led to the identification of 40 primary hit compounds. Five of these compounds were non-toxic to host cells and had similar activity against both C. caviae GPIC and Chlamydia trachomatis. The inhibitory activity of one of the compounds (3-methoxyphenyl)(4,4,7-trimethyl-4,5-dihydro-1H-[1,2]dithiolo[3,4-C]quinolin-1-ylidene)amine; MDQA) was chlamydia-specific and was selected for further study. Selection for resistance to MDQA led to the generation of three independent resistant clones of C. trachomatis. Amino acid changes in SecY, a protein involved in Sec-dependent secretion in Gram-negative bacteria, were associated with the resistance phenotype. The amino acids changed in each of the resistant mutants are located in the predicted central channel of a SecY crystal structure, based on the known structure of Thermus thermophilus SecY. These experiments model a process that can be used for the discovery of anti-chlamydial, anti-intracellular, or anti-bacterial compounds and has lead to the identification of compounds that may have utility in both antibiotic discovery and furthering our understanding of chlamydial biology.