Well, they are the same form factors, but the differences are as follows.
ATX12V all have 24 pin connectors, dual 12V rails, serial ATA connectors, and a minimum efficiency rating of 70% full power efficiency and a recommended rating of 80%.
They will work with ATX motherboards as they usually have a 20+4 pin connector, whereas ATX PSUs are only designed to work with the older systems.