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The Upper Quaternary seismic stratigraphy and active faults of the Gulf of Izmit were investigated by means of high-resolution shallow seismic profiling data in the source region of 1999 Izmit earthquake. High-resolution seismic reflection data correlated with borehole data indicate that the stratigraphy of Izmit Bay consists of three distinct depositional sequences formed in response to middle Pleistocene-Holocene sea-level changes. Reflector R, separating the pre-Holocene sequences (1 and 2) from the Holocene sequence (3), represents an erosional unconformity produced by the subaerial fluvial erosion of the continental shelves at the time of the last glacial maximum. Occasional, anomalous reflections (acoustic turbidity) observed within the Holocene sequence are interpreted as gas accumulations. The maximum thickness of the Holocene sediments is found to be about 25 m. The isopach map of Holocene sediment implies that the thickness of the Holocene decreases from the east towards the central and western basins of Izmit Bay. Two distinct fault systems are interpreted in Izmit Bay. The main fault system extending roughly in an E-W direction along the Gulf of Izmit is an active right lateral strike slip fault with a normal component. The secondary faults are normal faults striking in different directions and these are identified as being both active and inactive. In addition, prominent compressive features are identified in the seismic cross-sections of some profiles acquired to the east of Hersek Peninsula where the focal mechanisms of the aftershocks of the 1999 Izmit earthquake also reveal predominantly reverse faulting mechanisms, as identified by a local dense seismic network.