Use of Copan FLOQSwab due to its stronger capillary action should result in better specimen collection and more effective release of collected material. The objective of the present study was to evaluate FLOQSwab next to the swab validated by manufacturer in Abbott RealTime CT PCR for the detection of Chlamydia trachomatis. In total 1084 couples of both types of swabs were collected during 21 months as a part of the female sex workers’ screening programme. The study was devided in two arms according to the order of swab collection. If manufacturer’s swab was collected first, 32 coupled samples were both positive, 459 - both negative and 36 - discordant. Among discordant samples 25 (69%) required retesting of FLOQSwab (IC failed-flagging in 16 (44%) cases) with the final negative results. For 2 samples no result on FLOQSwab was available due to persistent inhibition while manufacturer’s swab gave negative results by initial testing. Two samples gave FLOQSwab positive/manufacturer’s swab negative results. When comparing analytical values of concordant positive samples, no statistical difference was oberved (p-value 0.49). If FLOQSwab was taken first, 32 coupled samples were both positive, 483 - both negative and 42 - discordant. Twenty one (50%) of the discordant results represented retesting of FLOQSwab due to the IC failed-flagging with the final negative results. The result for 1 FLOQSwab could not be achieved while the manufacturer’s swab was negative. Eight samples were positive only by FLOQSwab, 2 - only by manufacturer’s swab. Analytical values of concordant positive samples did not differ statistically (p-value 0.22). Concluding, FLOQSwab can be used for Abbott RealTime CT PCR. Positivity in 10 additional samples by FLOQSwab was in low analytical range while technical problems led to retesting of 46 FLOQSwab’s, for 3 FLOQSwab’s no final result was achieved and 2 low positives were missed.