We describe the first postnatal diagnosis of a child from Central Brazil with de novo cytogenetic alterations in 13q showing malformations of the brain, eyes, distal limbs, and genitourinary tract, and severe intellectual disability. The karyotype was a constitutive 46,XX,r(13)[77]/45,XX,-13[17]/46,XX,idic r(13)[6]. Interphase and metaphase fluorescence in situ hybridization analyses also showed the absence of 13qter and the presence of 13q14.3 in the cells with r(13), and chromosome microarray analysis detected a 15.39 Mb deletion in chromosome region 13q32.3-q34. This study is intended as the registry of a rare case of chromosomal rearrangement involving chromosome 13 in Central Brazil. Further studies are needed to define whether genetic haploinsufficiency is associated with each major 13q deletion anomaly.