The current concept of idiopathic scoliosis (IS) consists of a multifactorial disease involving genetic and non-genetic factors in the occurrence and progression of curvature. The candidate gene association study begins with selection of a putative candidate gene based on hypotheses, including biological systems involved in the development of deformity and assumptions based on results of clinical observations. The aim of a genome wide association study (GWAS) is to detect significant associations in a population between common diseases and common genetic variants. The results from previous association studies based on hypotheses and from whole genome scan suggest involvement of polymorphic variants of different candidate genes with different impact on the etiopathogenesis of IS in different population groups. The identification of molecular markers with diagnostic and prognostic value could be useful in clinical practice for early diagnosis of scoliosis among relatives and for more accurate prognosis of the risk of rapid progression of the deformity among affected individuals. That will permit prophylaxis and early treatment with less invasive procedures.