LIS1, a causative gene product for type I lissencephaly, binds to and regulates the dynein motor and the centrosome. LIS1 also forms a complex with the catalytic subunits α1 and α2 of type I platelet‐activating factor acetylhydrolase [PAF‐AH (I)]. However, the cellular function of the catalytic subunits remains unknown. In this study, we showed that over‐expression of the catalytic subunits, especially α2, in cultured cells induced dramatic phenotypical changes including nuclear shape change, centrosomal amplification and microtubule disorganization. We examined if these effects were due to the catalytic activity and/or binding of α2 to LIS1. Substitution of a single amino acid Glu39 of murine α1 and α2 by Asp (α2‐E39D) did not affect catalytic activity but completely abolished LIS1 binding. Over‐expression of either α2‐E39D or the catalytically inactive α2‐S48C revealed that α2‐E39D, but not α2‐S48C, lost its ability to induce above‐mentioned phenotypic changes. Biochemical analyses showed that LIS1 present in the precipitate fraction of murine brain homogenates could be translocated to the soluble fraction by α2, but not by α2‐E39D. These results suggest that over‐expression of the PAF‐AH (I) catalytic subunits induces centrosomal amplification and microtubule disorganization by disturbing intracellular localization of LIS1.