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Most of compact binary systems are expected to circularize before the frequency of emitted gravitational waves (GWs) enters the sensitivity band of the ground based interferometric detectors. However, several mechanisms have been proposed for the formation of binary systems, which retain eccentricity throughout their lifetimes. Since no matched-filtering algorithm has been developed to extract continuous GW signals from compact binaries on orbits with low to moderate values of eccentricity, and available algorithms to detect binaries on quasi-circular orbits are sub-optimal to recover these events, in this paper we propose a search method for detection of gravitational waves produced from the coalescences of eccentric binary black holes (eBBH). We study the search sensitivity and the false alarm rates on a segment of data from the second joint science run of LIGO and Virgo detectors, and discuss the implications of the eccentric binary search for the advanced GW detectors.