Phospholipid fatty acid (PLFA) analysis has gained great importance in the study of soil microbial community structure. This structure can give indication of the soil status. Purpose of the present paper is to analyse PLFA patterns in altered agricultural soils in order to develop a soil status alteration index. Soils subjected either to intensive agricultural exploitation, or to overflow by municipal and industrial wastes, or to irrigation with saline waters were analysed for PLFA content and compared to adjacent untreated soils by means of different statistical techniques. Principal component analysis separated PLFAs in three groups: unsaturated PLFAs (first axis, 48% of total variance), monounsaturated and cyclopropane PLFAs (second axis, 28% of total variance) and polyunsaturated PLFAs (third axis, 24% of total variance). By means of canonical discriminant analysis, a soil alteration index (SAI) was produced from 15 PLFAs using two data sets. A third data set was used to test the SAI general validity together with other data sets reported in literature. The index validity was confirmed in most cases: SAI gave higher scores for control soils and was generally able to classify soils according to their reported degree of alteration.