Abstract: Objective: To reveal the genetic cause of a child patient with muscular hypotonia, growth retardation and dull reaction. Methods: G banding karyotype analysis was performed by routine culture of peripheral blood lymphocyte from the child and his parents, then genome-wide chromosomal analysis for the family was carried out by SNP (single nucleotide polymorphisms) microarray. Results: The G banding karyotype of the child showed complex translocation in 4 chromosomes, described as 46, XY, t (2, 12, 18, 14) (q31, p13, q21.3, q11.2). SNP-array analysis indicated a deletion of 1.502 2×107 bp fragment at chromosome 18q21.31-q22.3 region, but there were no obvious abnormalities in the chromosomal karyotype and SNP-array analysis of the parents. The complex chromosomal structural abnormalities in the child should be de novo. Conclusion: The microdeletion of chromosomal 18q21.31-q22.3 and the complex translocation in 4 chromosomes might cause the phenotypes of disorders in the child. SNP-array should be helpful for revealing submicroscopic abnormalities in chromosomal translocation.