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Background: Brachycephalic dogs clinically affected by brachycephalic obstructive airway syndrome have been shown to have a high incidence of gastrointestinal disease, with French Bulldogs (FBD) identified as a particularly affected breed., Methods: Clinical records of 750 brachycephalic dogs attending over 500 practices participating in the small animal veterinary surveillance network (SAVSNET) project were analysed in this cohort study to determine the incidence of alimentary and respiratory disease within FBD, Bulldogs (BD) and Pugs attending primary care veterinary practice. Electronic clinical records were studied for treatment or acknowledgement of specific clinical signs that could be attributed to different anatomical locations. Disease of the different anatomical locations was marked as either being present or not present which allowed for statistical analysis., Results: Significant differences in the incidence of oesophageal (p = 0.006), gastric (p = 0.001) and intestinal (p = 0.001) diseases were present among the breeds studied. FBD had significantly increased odds ratios of having oesophageal (2.0, 2.2), gastric (2.4, 1.5) and intestinal (1.7, 1.5) diseases relative to Pugs and BD, respectively. Pugs had significantly increased odds ratios of having upper respiratory tract disease relative to BD (1.9)., Conclusion: The results show the incidence of gastrointestinal disease and upper respiratory tract disease is significantly different between the brachycephalic breeds studied. Furthermore, the general population of FBD has the highest incidence of gastrointestinal disease., (© 2022 The Authors. Veterinary Record published by John Wiley & Sons Ltd on behalf of British Veterinary Association.)