The majority of GC and NGC showed previous history of hydatiform mole. GC and NGC present different genomic profiles by aCGH. Recurrent losses involving CDH19 and TRIM32 were detected in GC. Gains of 17q25 (CBX2, CBX4 and CBX8) were preferentially found in high risk prognostic score in GC. In silico analysis revealed the involvement of PTEN and PI3K-Akt pathways in GC.