Acute gastroenteritis (AG) is frequently caused by infectious intestinal diseases (IID) including food- and waterborne pathogens of public health importance. Among these pathogens, Campylobacter spp. plays a major role. Many European countries monitor selected IIDs within disease surveillance systems. In Switzerland, the information on IIDs is restricted to limited surveillance data, while no data is available for AG. We conducted a qualitative study among Swiss general practitioners (GPs) to investigate the case management of AG and campylobacteriosis patients, the associated disease burden and the determinants leading to registration in the National Notification System for Infectious Diseases (NNSID). Interviews were conducted with a semi-structured questionnaire and underwent inductive content analysis based on Grounded Theory. The questionnaire was repeatedly adapted to capture emerging themes until the point of theoretical saturation. GPs perceived AG and campylobacteriosis of little relevance to their daily work and public health in general. According to GP self-estimates each consults about two cases of AG per week and diagnoses a median of five campylobacteriosis cases per year. A large proportion of AG cases receives telephone consultations only and gets medical advice from the practice nurse. Antibiotic therapy is considered useful and stool diagnostics are performed for about a fifth of consulting AG patients. Stool diagnostics ("test") and antibiotic therapy ("treat") are interrelated and follow four strategies: "Wait & See", "Treat & See", "Treat & Test", and "Test & See". AG case management is diverse and includes different triage steps. A small proportion of AG patients have stool diagnostics performed and only positive tested patients are reported to the NNSID. As a result severe cases and cases with a history of travel abroad are overrepresented in the NNSID. The use of multiplex PCR panels in routine diagnostics likely leads to improved case management and higher case numbers in surveillance systems.