In medical clinics, guidelines are the best ways for practitioners to make good decisions on patient's medical problems. There are different kinds of symptoms at all kinds of illnesses and this will affect the medicians' decision on the diagnosis/treatment. These guidelines are the results of an algorithm to follow and the ways to defeat the illness. These guidelines are developed in textual format. In order to process them in computer systems, a machine procesable format, called GLIF, is developed and this format is widely used througout the world. In this way, the clinical guidelines can be encoded in GLIF format and they can be used in hospital information systems. Currently, H1N1 pandemic flu (i.e. Swine flu) is a global threat. Only in Turkey, there are about 350 casualties as annouced by the Ministry of Health. Furthermore, Ministry of Health published a guideline towards the diagnosis and initial treatment of H1N1. However, it is in textual format; in other words it is not machine processable. In this paper, we have developed a system, called HINlDiagnose, to be used in the diagnosis of the H1N1 flu. In this respect, we first developed the GLIF format of the textual guideline and then implemented a guideline execution engine that process the guideline. In other words, this is an expert system that helps the practitioners for the analysis of patient data and make the diognosis. Indeed, the system is not specific to a single H1N1 guideline. It is generic in that it can process any guideline in GLIF format.