The atypical skin lesions are a diverse group of tumours that are uncommon but clinically important. They include a spectrum from benign lesions through to those that demonstrate local invasion and/or distant metastatic potential. Since these lesions are only seen infrequently during clinical practice, it is important to have a solid grounding in the general principles of their management. We also cover some common surgically relevant lesions of the skin, including common types of cysts. A clear understanding of cysts and their aetiology is important to direct their management. We have divided the atypical lesions into benign or malignant and then by their cell/tissue of origin to provide a framework for their study. Such a framework is not perfect due to our evolving understanding of the molecular and cellular bases of these tumours, but it provides a foundation for their study.