The primary difference between an autotransformer and an isolation transformer lies in their construction and function. An autotransformer has a single winding that serves as both the primary and secondary, allowing for voltage adjustment with a shared portion of the winding. In contrast, an isolation transformer has separate primary and secondary windings, providing electrical isolation between input and output. This isolation enhances safety and reduces noise, making isolation transformers ideal for sensitive equipment, while autotransformers are more efficient for voltage conversion.