The main difference among ATX and BTX motherboards is the position of the slots. BTX motherboards are like mirrored ATX boards. Where the connectors of the serial ports, parallel ports, keyboard, mouse, USB, etc. are soldered today we find the expansion slots in the BTX boards. And where the expansion slots are today, in BTX motherboards we find the board connectors (serial ports, parallel ports, keyboard, mouse, USB, etc.)
Another difference is the distance between the motherboard and the metallic chassis of the PC case, which is 0.4173 in. (10.6 mm), bigger than the distance in the ATX standard, which improves the flow of air in lower part of motherboard and facilitates the use of systems to fit in the cooler of larger processors.