It is well established that GAA/TTC base triplet expansion is the cause of degenerative disorder in Freidreich?s Ataxia. It is also known that these repeat sequences fold back to form the unusual intramolecular triple helix structures in DNA of the type Pyrimidine*Purine·Pyrimidine or Purine*Purine·Pyrimidine. In this paper we report on the stability of Purine*Purine·Pyrimidine intermolecular triple helix DNA containing GAA/TTC repeats under physiological conditions. Using the oligonucleotides 5? TCGC GAA GAA GAA GAA GAA CGCT 3?, 5?-AGCG TTC TTC TTC TTC TTC GCGA-3? for duplex and 5?- AAG AAG AAG AAG AAG -3? as triplex forming strand (TFO), we have established the formation of triplex by UV?melting temperature (Tm), stoichiometry of mixing and circular dichroic spectra. This was further confirmed by gel-retardation assay. The thermodynamic parameters ΔG, ΔH and ΔS for both duplex and triplex formation were determined at different salt concentrations. The results suggest the formation of a stable intermolecular, anti-parallel triplex in GAA/TTC repeat sequences where each repeat unit contains two A*A·T and one G*G·C triplet. The therapeutic agents and TFOs, which competitively inhibit the in vivo intra-molecular triplex by formation of a more stable inter-molecular triplex, could be used to reverse the transcription deficit in GAA/TTC expansions in Frataxin gene.