The main functions of a motherboard in a computer system include acting as the primary circuit board that connects all components. It hosts the CPU, memory, and expansion slots, facilitating communication between the processor and peripherals. The motherboard also features integrated chipsets that manage data flow and connectivity options. Power distribution is another critical function, supplying energy to different hardware components. Additionally, it provides ports for external connections such as USB, audio, and video, making it central to the overall functionality and performance of a computer.