The invention relates to a system for short pulse laser eye surgery (100) comprising a short pulse laser system (200), an operational microscope (300) and a control unit (500), a housing (110) and a first articulated arm (120) on which a microscope head (320) of the operational microscope (300) is fixed and a second articulated arm (130) on which the applicator head (220) of the short-pulse laser system (200) is fixed, said two heads can be connected to each other. The invention also relates to a patient interface (600) and to a computer program product for coding a control unit (500) of the system. The invention further relates to a method for positioning an applicator head (220) and a microscope head (320), to methods for carrying out incisions using a short pulse laser system for eye surgery and referencing methods. The aim of the invention is to provide systems and methods for short pulse laser eye surgery in which the quality of operating result and also the typical operating sequence are improved, as well as improving the efficiency of the operating procedure and the safety of the operation. Said aim is achieved by means of a system for short-pulse laser eye surgery (100) and a short pulse laser system (200) comprising beam guiding means (230) which pass through the corresponding articulated arm (130), and due to the applicator head (220) and a microscope head (320) of the system which can be moved in a three-dimensional volume independently from each other as well as connected together, also due to an easy to handle patient interface (600) having a one-part contact glass (610), a computer programme product for the methods for carrying out the incision and to sequentially working referencing methods with patient interfaces (600) which contain the markings.