In Xenopus development the mid-blastula transition (MBT) marks a dramatic change in response of the embryo to ionizing radiation. Whereas inhibition of cyclin D1-Cdk4 and cyclin A2-Cdk2 by p27(Xic1) has been linked to cell cycle arrest and prevention of apoptosis in embryos irradiated post-MBT, distinct roles for these complexes during apoptosis are evident in embryos irradiated pre-MBT. Cyclin A2 is cleaved by caspases to generate a truncated complex termed Delta N-cyclin A2-Cdk2, which is kinase active, not inhibited by p27(Xic1), and not sensitive to degradation by the ubiquitin-mediated proteasome pathway. Moreover, Delta N-cyclin A2-Cdk2 has an expanded substrate specificity and can phosphorylate histone H2B at Ser-32, which may facilitate DNA cleavage. Consistent with a role for cyclin A2 in apoptosis, the addition of Delta N-cyclin A2-Cdk2, but not full-length cyclin A2-Cdk2, to Xenopus egg extracts triggers apoptotic DNA fragmentation even when caspases are not activated. Similarly, cyclin D1 is targeted by caspases, and the generated product exhibits higher affinity for p27(Xic1), leading to reduced phosphorylation of the retinoblastoma protein (pRB) during apoptosis. These data suggest that caspase cleavage of both cyclin D1-Cdk4 and cyclin A2-Cdk2 promotes specific apoptotic events in embryos undergoing apoptosis in response to ionizing radiation.