Persistence of Chlamydia trachomatis (C. trachomatis) in the joint is the most frequent cause of reactive arthritis following urogenital tract infection. The resulting changes of host cell antigen- and cytokine-expression are not precisely understood. We developed and evaluated a direct cytometric approach to visualize in vitro C. trachomatis-infected monocytes. Infectious elementary bodies (EBs) of C. trachomatis serovar K were labelled by incubation with 5-(and-6)-carboxyfluorescein diacetate succinimidyl ester (CFSE). Afterwards, human peripheral blood monocytes were cultured with the CFSE-labelled EBs and analysed by flow cytometry. Real-time polymerase chain reaction (PCR) was used to demonstrate intracellular uptake and viability of CFSE-labelled C. trachomatis by the determination of gene expression. Labelling EBs with CFSE may become a valuable tool for studying the interaction between C. trachomatis and the host cell.