The ML 5.4 Molise earthquake of 31 October 2002 caused damage of Mercalli-Cancani-Sieberg (mcs) intensity VIII–IX to the small town of San Giuliano di Puglia. In contrast, the other towns in the epicentral area did not exceed mcs intensity VII. Building vulnerability and near-surface geology were suspected to be potentially responsible for the high level of damage. However, early results of engineering studies in San Giuliano di Puglia (Dolce et al., 2004) indicate that vulnerability of the strongest damage [European Macroseismic Scale, (ems) intensity VII–VIII] zone was not higher than vulnerability of the remaining part of the town (ems intensity VI). We use the aftershock recordings in the town to investigate the local amplification effect due to the lateral variations of near-surface geology. The waveform analysis shows that in the high-damage zone, where clay deposits outcrop, direct S waves are characterized by a large initial pulse that is a factor of 6 larger than S waves recorded on a nearby rock outcrop, a few hundred meters away. Moreover, the strong S pulse is followed by a 10-sec long amplification of ground motion between 4 and 7 Hz. This frequency band corresponds to the fundamental resonance frequencies of two- and three-storied buildings, which are the most common type of construction in San Giuliano di Puglia. Since the duration of the strongest shaking is estimated to have been longer than 10 sec during the main shock, we conclude that the highly damaging effect in the clayey zone could have been due to the combination of the large initial pulse with time-persistent amplification at the resonant frequencies of buildings.