Nek2 is a cell-cycle-regulated protein kinase that localizes to the centrosome and is likely to be involved in regulating centrosome structure at the G(2)/M transition. Here, we localize the functional human Nek2 gene to chromosome 1 and show that alternative polyadenylation signals provide a mechanism for generating two distinct isoforms. Sequencing of products generated by reverse transcriptase PCR, immunoblotting of cell extracts and transfection of antisense oligonucleotides together demonstrate that human Nek2 is expressed as two splice variants. These isoforms, designated Nek2A and Nek2B, are detected in primary blood lymphocytes as well as adult transformed cells. Nek2A and Nek2B, which can form homo- and hetero-dimers, both localize to the centrosome, although only Nek2A can induce centrosome splitting upon overexpression. Importantly, Nek2A and Nek2B exhibit distinct patterns of cell-cycle-dependent expression. Both are present in low amounts in the G(1) phase and exhibit increased abundance in the S and G(2) phases. However, Nek2A disappears in prometaphase-arrested cells, whereas Nek2B remains elevated. These results demonstrate that two alternative splice variants of the human centrosomal kinase Nek2 exist that differ in their expression patterns during mitosis. This has important implications for our understanding of both Nek2 protein kinase regulation and the control of centrosome structure during mitosis.