Main shock and aftershock accelerograms from the Loma Prieta earthquake sequence are analyzed to study relative ground amplification at sites in the city of San Francisco. Main shock spectra are estimated for those stations that recorded only aftershocks by comparing their records to those from stations that recorded both. The ratios of the spectra with respect to a stable bedrock station located at Fort Mason show distinct spectral shapes that are strongly correlated with the rock type underlying the site. Earthquake damage is quantified using estimates of the Modified Mercalli Intensity at the recording sites and safety tags issued by the City of San Francisco Building Department. These intensities are compared with ground amplification in three frequency bands and with the intensities at the same sites from the 1906 San Francisco earthquake. There is sufficient correlation to show that site amplification is one of the controlling factors in damage distribution.