MOTIVATION: The centrosome is a dynamic structure in animal cells that serves as a microtubule organizing center during mitosis and also regulates cell-cycle progression and sets polarity cues. Automated and reliable tracking of centrosomes is essential for genetic screens that study the process of centrosome assembly and maturation in the nematode Caenorhabditis elegans. RESULTS: We have developed a fully automatic system for tracking and measuring fluorescently labeled centrosomes in 3D time-lapse images of early C. elegans embryos. Using a spinning disc microscope, we monitor the centrosome cycle in living embryos from the 1- up to the 16-cell stage at imaging intervals between 30 and 50 s. After establishing the centrosome trajectories with a novel method involving two layers of inference, we also automatically detect the nuclear envelope breakdown in each cell division and recognize the identities of the centrosomes based on the invariant cell lineage of C. elegans. To date, we have tracked centrosomes in over 500 wild type and mutant embryos with almost no manual correction required. AVAILABILITY: The centrosome tracking software along with test data is freely available at http://publications.mpi-cbg.de/itemPublication.html?documentId=4082.