Objectives In 2006, a new variant of Chlamydia trachomatis (nvCT) was reported in Sweden. Because of a cryptic plasmid deletion, the nvCT was undetectable in several of the genetic diagnostic systems used worldwide at the time. This study aimed to evaluate whether the nvCT was present in specimens obtained from patients attending the outpatient sexually transmitted infection (STI) clinic at orebro University Hospital, orebro, Sweden already in 2002-2003. Methods In 2012, archival (-20 degrees C freezer) urogenital specimens (2002 (n=1083) and in 2003 (n=1143)) obtained from men (2002 (n=398) and 2003 (n=486)) and women (2002 (n=301) and 2003 (n=408)) were analysed with Cobas TaqMan CT test V.2.0. All C trachomatis positive specimens were subsequently examined using a duplex PCR assay that simultaneously detects the deletion on the nvCT cryptic plasmid and the ompA gene of C trachomatis genotype E. Results In total, 68 patients (9.7%) in 2002 and 61 (6.8%) in 2003 were C trachomatis positive. The duplex PCR assay identified 26 C trachomatis genotype E positive patients in 2002 (38%) and 25 in 2003 (41%). No nvCT was found in 2002, but one specimen obtained from a 23-year-old man in June 2003 was positive for the nvCT. Conclusions The nvCT was present as early as 2003 in orebro County, Sweden, which concurs with previously reported statistical estimations of its emergence. Accordingly, the nvCT spread undetected for at least 3years, explaining the high proportion (38%) in orebro County when it was first detected in late 2006.