He is best known for his tinted photographs of dreamy worlds filled with naked or half-naked figures against a peeling wall, often reproducing the same elements and symbols. This was partly out of sheer necessity because he only had the cellar at his disposal and could not store much stuff in it. His photographs are reminiscent of mid-19th century erotic photography and the work of painters such as Balthus and Bernard Faucon. In his early days it is mainly about depicting youth, later the theme shifts to the development from youth to adulthood and old age (following the subject in the same composition over several years). Religion and the ambiguity between man and woman are also recurring themes in Jan Saudek's work. His work became the subject of censorship in the West in the 1990s.

Some of his photos appeared on album covers. Such as Anorexia Nervosa (New Obscurantis Order), Soul Asylum (Grave Dancers Union), Daniel Lanois (For the Beauty of Wynona) and Beautiful South (Welcome to the Beautiful South).