Non-random distribution of more than 1 million Alu elements in the human genome suggests their structural and/or functional role. Numerous efforts have not succeeded in clarifying the structural organization and evolution of Alu elements. The Alu elements are mainly composed of two monomers: left (L) and right (R). This study demonstrates the invariant secondary structures of the Alu repeats. These structures allow high diversity of compensatory mutations. On the other hand, conservative secondary structures appear important for the functioning of Alu repeats in the human genome. The tetraplex GC-rich clusters GGGC and GCCC were identified in the dimeric Alu repeats and shown to form a unique core structure in both L and R monomers. Medium-scale interactions (triplex structures) were found between the GC-rich clusters, and the fine structure of the repeated and complementary modules within the Alu elements was analyzed. All Alu repeats were shown to contain invariant tRNA-like structures. The core Alu model may be applied at a higher chromosomal level when mono-, di-, and trimeric Alu forms are considered as interacting units. The set of Alu elements in the human genome may be regarded as a dynamic system. Reording and selection of the Alu interactions at both the DNA and the chromosomal scale may be described with a certain chromosomal code.