The　inositol　polyphosphate-5-phosphatase　E　(Inpp5e)　gene　is　located　on　chromosome　9q34.3.　The　enzyme　it　encodes　mainly　hydrolyzes　the　5-phosphate　groups　of　phosphatidylinositol　(3,4,5)-trisphosphate　(PtdIns　(3,4,5)　P3)　and　phosphatidylinositol　(4,5)-bisphosphate　(PtdIns　(4,5)P2),　which　are　closely　related　to　ciliogenesis　and　embryonic　neurodevelopment,　through　mechanisms　that　are　largely　unknown.　Here　we　studied　the　role　of　Inpp5e　gene　in　ciliogenesis　during　embryonic　neurodevelopment　using　inositol-deficiency　neural　tube　defects　(NTDs)　mouse　and　cell　models.　Confocal　microscopy　and　scanning　electron　microscope　were　used　to　examine　the　number　and　the　length　of　primary　cilia.　The　dynamic　changes　of　Inpp5e　expression　in　embryonic　murine　brain　tissues　were　observed　during　Embryonic　Day　10.5-13.5　(E　10.5-13.5).　Immunohistochemistry,　western　blot,　polymerase　chain　reaction　(PCR)　arrays　were　applied　to　detect　the　expression　of　Inpp5e　and　cilia-related　genes　of　the　embryonic　brain　tissues　in　inositol　deficiency　NTDs　mouse.　Real-time　quantitative　PCR　(RT-qPCR)　was　used　to　validate　the　candidate　genes　in　cell　models.　The　levels　of　inositol　and　PtdIns(3,4)　P2　were　measured　using　gas　chromatography-mass　spectrometry　(GC-MS)　and　enzyme　linked　immunosorbent　assay　(ELISA),　respectively.　Our　results　showed　that　the　expression　levels　of　Inpp5e　gradually　decreased　in　the　forebrain　tissues　of　the　control　embryos,　but　no　stable　trend　was　observed　in　the　inositol　deficiency　NTDs　embryos.　Inpp5e　expression　in　inositol　deficiency　NTDs　embryos　was　significantly　decreased　compared　with　the　control　tissues.　The　expression　levels　of　Inpp5e　gene　and　the　PtdIns　(3,4)　P2　levels　were　also　significantly　decreased　in　the　inositol　deficient　cell　model.　A　reduced　number　and　length　of　primary　cilia　were　observed　in　NIH3T3　cells　when　inositol　deficient.　Three　important　cilia-related　genes　(Ift80,　Mkks,　Smo)　were　down-regulated　significantly　in　the　inositol-deficient　NTDs　mouse　and　cell　models,　and　Smo　was　highly　involved　in　NTDs.　In　summary,　these　findings　suggested　that　down-regulation　of　Inpp5e　might　be　associated　with　abnormal　ciliogenesis　during　embryonic　neurodevelopment,　under　conditions　of　inositol　deficiency.