We estimated the prevalence of the new variant of Chlamydia trachomatis in Denmark. Fifty consecutive C trachomatis urine samples from each of the 14 regional microbiology laboratories were initially tested and re-analysed with a real-time C trachomatis PCR assay targeting the 16S rRNA gene and with the Becton Dickinson ProbeTec with confirmation of positives with a plasmid PCR with the primers CTP200/CTP201 flanking the deletion. The positive rate for 691 samples was 17% by real-time C trachomatis PCR and by ProbeTec. One specimen was positive for the new variant of C trachomatis (0.14% of all samples; 0.8% of the positives). The prevalence of the new variant of C trachomatis is very low despite very close contact between Denmark and Sweden and extensive cross-border commuting.