Dengue disease is caused by dengue viruses 1-4 and has been ranked by the World Health Organisation (WHO) as the fastest spreading vector-borne viral disease. Dengue is often underreported and misdiagnosed due to a wide spectrum of clinical manifestations. Diagnosis of dengue is based on clinical case definitions and laboratory methods. Newer case definitions of dengue have been formulated by clinical studies in order to improve case detection. Owing to its epidemic potential, mortality and morbidity, there is a need for a rapid and accurate diagnostic assay for dengue in order to help the clinician in the early detection of cases and to prevent disease progression. A duplex real time PCR targeting the 3'UTR region for rapid and simultaneous detection of all dengue viruses serotypes (1-4) was standardized based on published literature. About 150 patients with acute undifferentiated febrile illness classified based on the 2009 WHO dengue case definition were tested using the duplex real time dengue PCR. Sequencing based PCR was performed on selected PCR positive samples for partial nucleotide sequence of the CprM gene and a phylogenetic tree was constructed. Statistical analysis was done using the MedCalc software. Out of the 126 patients classified as dengue disease positive, according to the 2009 WHO dengue case definition, 54% had "probable dengue", 43% had "dengue with warning signs" and 3% had "severe dengue". The performance of the duplex real time PCR was assessed among the various clinical groups of dengue and it was found that in the "dengue with warning signs group" PCR had a positive predictive value of 85.29% (range - 68.94% to 95.05%) when compared with dengue NS1 ELISA. The average time for PCR positivity was found to be four days from the onset of illness. The cycling threshold values obtained from real time PCR were used as a semi quantitative measure of viremia. Accordingly, there was a relatively low CT value among the "warning signs dengue group" when compared to the "probable dengue group". The use of the duplex PCR is suggested in the early diagnosis of dengue, especially in the 'warning signs' group of patients as they showed a higher positivity rate. Also, the use of the resultant CT value as a semi-quantitative measure of viremia will assist the clinician in early diagnosis and prevention of disease development.