Three bacterial isolates named, CdSP9 (Ochrobactrum sp.), PbSP6 (Bacillus sp.) and AsSP9 (Bacillus sp.) resistant to cadmium, lead and arsenic salts, have been characterized in this study on the basis of the changes in their total fatty acid composition under respective heavy metal stress. A general increase of saturated fatty acids was observed in presence of metal. In cadmium treated CdSP9, the saturated fatty acids, C14:0 and C16:0 and unsaturated fatty acids C14:1, C18:1cis and C18:2cis were formed in increased amounts and two short chain saturated fatty acids, C12:0 and C13:0 were expressed exclusively. In PbSP6, fatty acids C15:0, C16:0 and C17:0 were significantly increased in presence of lead, while C11:0 was expressed under treated condition only. Regarding AsSP9, the unsaturated fatty acids like C18:1cis, C18:2cis were predominantly formed under arsenic treated condition and the omega-3 fatty acid C18:3n3, which is not found in other two strains, was exclusively expressed in AsSP9, though in absence of the metalloid. These changes in the fatty acid composition are in response to the given heavy metal/metalloid stress and their role in defence against heavy metal toxicity seems very significant.