Refs and atoms shouldn't have side effects, but agents are great for performing side effects. From page 214 of Clojure Programming:

    Unlike refs and atoms, it is perfectly safe to use agents to coordinate 
    I/O and perform other blocking operations. This makes them a vital
    piece of any complete application that use refs and Clojure’s STM
    to maintain program state over time. Further, thanks to their semantics,
    agents are often an ideal construct for simplifying asynchronous
    processing involving I/O even if refs are not involved at all.

Further:

    Agents are integrated into Clojure’s STM implementation such that
    actions dispatched using send and send-off from within the scope
    of a transaction will be held in reserve until that transaction
    is successfully committed. This means that, even if a transaction
    retries 100 times, a sent action is only dispatched once, and that
    all of the actions sent during the course of a transaction’s
    runtime will be queued at once after the transaction commits.