Trachoma, caused by the bacteria Chlamydia trachomatis, is the world leading infectious cause of blindness. The disease is associated with poor living conditions, especially in developing countries. In these countries, diagnosis is usually based on clinical evaluation, although laboratory confirmation is necessary. Serological-based tests for trachoma laboratory confirmation are cheaper than molecular-based tests, but the later are more sensitive and specific. Among the available molecular tests, qPCR has the best cost-benefit. With this in mind, the present study developed a new duplex qPCR reaction, which concomitantly detects C. trachomatis cryptic plasmid and the human 18S rRNA gene, as an internal reaction control. The new qPCR was validated using 50 previously qPCR-characterized samples for trachoma infection, and showed 95% specificity and 100% sensitivity, with an estimated LOD95 of 600 ag/µL. Next, 50 samples from an endemic area (Marajó, Pará) and 12 from a non-endemic area (Curitiba, Paraná) were investigated using direct immunofluorescence assay (DFA) or the new duplex qPCR. Among the 50 endemic samples, three were positive by clinical evaluation (6%), 18 by DFA (36%) and 48 by qPCR (96%). All samples positive by the clinic evaluation were also positive by qPCR. From the 18 DFA-positives, qPCR identified 16 as positives as well. On the other hand, 32 samples that were DFA-negative due to the low number of elementary bodies (<5 per slide) were positive by qPCR. The results show that the new duplex qPCR has sensitivity and specificity in similar levels to commercial qPCR tests available, and that qPCR indeed is more sensitive than clinical evaluation or DFA, thus allowing earlier treatment start. The ubiquitous presence of C. trachomatis DNA in samples from the endemic region confirms that constant monitoring is necessary. Additionally, effective measures for the elimination of trachoma and the detection of bacterial DNA in the active infection are of fundamental importance, and this newly developed duplex qPCR is an important tool towards this goal.