Inhibition of DNA synthesis prevents mitotic entry through the action of the S-phase checkpoint. We have isolated S-phase arrest-defective (sad) mutants that show lethality in the presence of the DNA synthesis inhibitor hydroxyurea (HU). Several of these mutants show phenotypes consistent with inappropriate mitotic entry in the presence of unreplicated DNA, indicating a defect in the S-phase checkpoint. sad1 mutants are additionally defective for the G1 and G2 DNA damage checkpoints, and for DNA damage-induced transcription of RNR2 and RNR3. The transcriptional response to DNA damage requires activation of the Dun1 protein kinase. Activation of Dun1 in response to replication blocks or DNA damage is blocked in sad1 mutants. The HU sensitivity of sad1 mutants is suppressed by mutations in CKS1, a subunit of the p34CDC28 kinase, further establishing a link between cell cycle progression and lethality. sad1 mutants are allelic to rad53, a radiation-sensitive mutant. SAD1 encodes an essential protein kinase. The observation that SAD1 controls three distinct checkpoints suggests a common mechanism for cell cycle arrest at these points. Together, these observations implicate protein phosphorylation in the cellular response to DNA damage and replication blocks.