A method and system are provided for storage checkpointing in a mirrored virtual machine system. The method includes a storage controller receiving a modifying operation to storage from a virtual machine and carrying out the modifying operation in a non-destructive manner by saving the modifying operation data to a checkpointing region of storage and preserving the stored previous data state. The method also includes receiving a checkpoint notification and committing modifying operation data from the checkpointing region and releasing the stored previous data state. If a failover notification is received, the storage controller rolls back the physical storage to match a checkpoint state.