Hydropathy profile alignment is introduced as a tool in functional genomics. The architecture of membrane proteins is reflected in the hydropathy profile of the amino acid sequence. Both secondary and tertiary structural elements determine the profile which provides enough sensitivity to detect evolutionary links between membrane proteins that are based on structural rather than sequence similarities. Since structure is better conserved than amino acid sequence, the hydropathy profile can detect more distant evolutionary relationships than can be detected by the primary structure. The technique is demonstrated by two approaches in the analysis of a subset of membrane proteins coded on the Escherichia coli and Bacillus subtilis genomes. The subset includes secondary transporters of the 12 helix type. In the first approach, the hydropathy profiles of proteins for which no function is known are aligned with the profiles of all other proteins in the subset to search for structural paralogues with known function. In the second approach, family hydropathy profiles of 8 defined families of secondary transporters that fall into 4 different structural classes (SC-ST1-4) are used to screen the membrane protein set for members of the structural classes. The analysis reveals that over 100 membrane proteins on each genome fall in only two structural classes. The largest structural class, SC-ST1, correlates largely with the Major Facilitator Superfamily defined before, but the number of families within the class has increased up to 57. The second large structural class, SC-ST2 contains secondary transporters for amino acids and amines and consists of 12 families.