Background: Indonesia is a country with high endemicity of dengue (haemorrhagic) fever (DF/ DHF). It was reported that dengue virus type 2 (DENV2) was the predominant circulating virus in 2003-2005 in Surabaya, Indonesia, while Yamanaka et al., 2011 reported shifting of DENV serotypes between 2008 - 2010 in three times survey. This study was part of the clinical trial phase three of antivirus against dengue, held in year 2012-2013. Methods: A total of 317 serum samples were collected from patients with fever on day-1 or day-2, suspected dengue infection according to WHO criteria, showed positive result either by NS-1, and or IgM - IgG within March 2012 - April 2013. After an RNA extraction, a multiplex DEN 1-4 quantitative Real-Time PCR was applied to each sample. Results: Sixty three (90%) of 70 PCR positive sera collected within March 2012 and May 2012 showed DENV2, then 5(7.2%) DENV1, 1(1.4%) DENV3, and 1mixed of DENV1+3. Surprisingly, it was totally different for those collected since June 2012 until April 2013. Fifty three (50%) of 106 positive samples were DENV1, 5 (4.7%) DENV2, 35 (33%) DENV3, 7 (6.6%) DEN4, and 2, 2, 1 mixed type of DENV 1+3, DENV1+4, DENV 3+4 respectively. Conclusions: There was a displacement of the predominant type of dengue virus circulating in Surabaya within March 2012 - April 2013. Such kind of predominant DENV shifting from type 2 to type 1 has occurred between October and November 2008. This indicates the need for continuous surveillance of the circulating viruses, which may predict the risk of severe DHF and mild DF as reported previously.