Quinolone resistance of chlamydiae is supposed to be extremely rare. To assess the risk for the emergence of chlamydial quinolone resistance, we analysed the occurrence of resistant mutants in a quantitative perspective. Infectious elementary bodies of Chlamydia trachomatis serovar L2 (ATCC VR-902B) and D (ATTC VR-885) clones were purified on density gradients, and mutants resistant to moxifloxacin and rifampicin were selected by a plaque assay. Plaque assays were conducted with 2 × 109 inclusion forming units (IFUs) of each serovar for rifampicin and 2.66 × 109 IFUs for moxifloxacin. Resistant clones were analysed for mutations in the gyrA, gyrB, parC and parE genes, and respective MICs were determined by titration experiments. Mutation frequencies for rifampicin (MIC ≥ 0.2 mg/L) did not differ significantly between serovars L2 and D (5.7 × 10−7 versus 6.3 × 10−7). In contrast, the occurrence of moxifloxacin-resistant mutants (MIC ≥ 0.6 mg/L) was determined to be 2.0–2.2 × 10−8 for the serovar L2 isolate and less than 2.66 × 10−9 for the serovar D isolate. Moxifloxacin resistance of all serovar L2 clones depended on single-nucleotide point mutations in the quinolone resistance-determining region of the gyrA, whereas no additional mutations were found in the gyrB, parC or parE genes. C. trachomatis isolates have the potential to present with clinically relevant antibiotic resistance in future. Serovar-specific differences in the occurrence of spontaneous mutations should be taken into account to predict quinolone resistance in different chlamydial diseases.