Imatinib is broadly used in the frontline treatment of chronic myeloid leukemia (CML). Although long-term safety and efficacy have been established, some patients will not respond to imatinib. Nilotinib and dasatinib successfully recapture responses for most patients with imatinib-refractory or -intolerant disease. These drugs have different safety profiles, which are likely associated with their divergent inhibitory targets. The presence of Bcr-Abl mutations and safety profiles of available therapies in relation to patient history should be considered when choosing a second-line agent. This review evaluates the safety and tolerability of agents approved for CML treatment and briefly discusses newer third-line agents.