We discuss the subsurface structure of the Karadere-Duzce branch of the North Anatolian Fault based on analysis of a large seismic data set recorded by a local PASSCAL network in the 6 months following the Mw = 7.4 1999 Izmit earthquake. Seismograms observed at stations located in the immediate vicinity of the rupture zone show motion amplification and long-period oscillations in both P- and S-wave trains that do not exist in nearby off-fault stations. Examination of thousands of waveforms reveals that these characteristics are commonly generated by events that are well outside the fault zone. The anomalous features in fault-zone seismograms produced by events not necessarily in the fault may be referred to generally as fault-zone-related site effects. The oscillatory shear wave trains after the direct S arrival in these seismograms are analysed as trapped waves propagating in a low-velocity fault-zone layer. The time difference between the S arrival and trapped waves group does not grow systematically with increasing source-receiver separation along the fault. These observations imply that the trapping of seismic energy in the Karadere-Duzce rupture zone is generated by a shallow fault-zone layer. Traveltime analysis and synthetic waveform modelling indicate that the depth of the trapping structure is approximately 3-4 km. The synthetic waveform modelling indicates further that the shallow trapping structure has effective waveguide properties consisting of thickness of the order of 100 m, a velocity decrease relative to the surrounding rock of approximately 50 per cent and an S-wave quality factor of 10-15. The results are supported by large 2-D and 3-D parameter space studies and are compatible with recent analyses of trapped waves in a number of other faults and rupture zones. The inferred shallow trapping structure is likely to be a common structural element of fault zones and may correspond to the top part of a flower-type structure. The motion amplification associated with fault-zone-related site effects increases the seismic shaking hazard near fault-zone structures. The effect may be significant since the volume of sources capable of generating motion amplification in shallow trapping structures is large.