In some cases, yes. Generally, the police need a warrant to search a person’s vehicle. However, there are many exceptions.
For example, if the police notice illegal drugs or weapons in your vehicle at the checkpoint, they can search your vehicle. If you are arrested, they may also perform an inventory search while preparing to have it towed.
In some cases, exigent circumstances may also justify a warrantless search of your vehicle at a DUI checkpoint. Exigent circumstances are instances when an imminent threat of harm or destruction of evidence exists.