Despite one SINE retrotransposon insertion polymorphism (sRTIP) in the vertebrae development-associated (VRTN) gene was identified in pigs, the structural variations (SVs) in VRTN gene and its proximal flank regions were largely unknown. VRTN genic and flanking sequences from 14 breeds were assembled or downloaded from whole-genome shotgun contings (WGS) database, and aligned to identify the SVs with Clustalx, and retrotransposons in VRTN gene were annotated by RepeatMasker, the splicing patterns of VRTN gene were predicted by Genescan, and large SVs were evaluated by PCR. A total of 12 small SVs and three large SVs in intron of VRTN, derived from SINE insertion polymorphisms, were identified, and two of them (VRTN-sRTIP2 and VRTN-sRTIP3) were not reported before. These VRTN-sRTIPs may affect the splicing patterns of VRTN. They displayed polymorphisms in most detected eight breeds. VRTN-sRTIP2 and VRTN-sRTIP3 showed Hardy-Weinberg equilibrium distributions in most populations except the Chinese local Erhualian pigs, while VRTN-sRTIP1 showed genetic equilibrium in Erhualian pigs. Three VRTN-sRTIPs were identified, and displayed polymorphisms in pigs, and two of them were not reported before. These SVs provide a useful molecular markers for genetic analysis in pigs, and offer new information to facilitate the understanding the SVs of VRTN gene and their putative roles in the variation of vertebral number.