Phosphatidylinositol-(4,5)-bisphosphate (PtdIns(4,5)P2) and phosphatidylinositol-(3,4,5)-triphosphate (PtdIns(3,4,5)P3) in the plasma membrane (PM) play a key role in the regulation of various cellular processes including proliferation, differentiation and survival. Their main role is to recruit a variety of signaling proteins to the PM via direct interaction with specific lipid binding domains (LBDs) and motifs in the proteins. In this study, I examined the subcellular localization of 94 distinct LBDs in order to better understand how PtdIns(4,5)P2 and/or PtdIns(3,4,5)P3 target different proteins to the PM and control their function. Surprisingly, I found that the FYVE domain of ZFYVE27 localizes to the PM. Surface plasmon resonance analysis shows that unlike canonical FYVE domains that specifically bind to phosphatidylinositol-3-phosphate this FYVE domain preferentially interacts with PtdIns(4,5)P2, PtdIns(3,4)P2 and PtdIns(3,4,5)P3 using basic amino acids inside the lipid-binding pocket. Furthermore, I found that PtdIns(4,5)P2 and PtdIns(3,4)P2/PtdIns(3,4,5)P3 differentially regulate ZFYVE27 shuttling from ER to PM via the FYVE domain. ZFYVE27 mutants with reduced affinity for PtdIns(4,5)P2, PtdIns(3,4)P2 and PtdIns(3,4,5)P3 failed to target the PM in NIH3T3 cells and promote neurite outgrowth in primary cultured hippocampal neurons. These results suggest that the novel PtdIns(4,5)P2 and PtdIns(3,4)P2/PtdIns(3,4,5)P3 selectivity of the FYVE domain of ZFYVE27 is critical for the role of ZFYVE27 in mediating neurite outgrowth.