Abstract Background Gastrointestinal diseases can have oral manifestations. The aim of this study was to investigate the knowledge of gastroenterologists and dentists about gastrointestinal diseases with oral manifestations and to assess the frequency, extent and content of communication between gastroenterologists and oral healthcare professionals. Methods Separate questionnaires were developed and sent to all 523 gastroenterologists and a random selection of 500 dentists in the Netherlands. Both questionnaires contained questions about demographic characteristics of the participants, 10 statements about gastrointestinal diseases with possible oral manifestations and questions about the communication between gastroenterologists and oral healthcare professionals. Additionally, the questionnaire for gastroenterologists contained 9 statements about general dentistry and the questionnaire for dentist had 9 questions about gastrointestinal diseases. Results Gastroenterologists answered 47.6% ± 31.9% of the questions correct about gastrointestinal diseases with possible oral manifestations and 57.5% ± 27.9% of the questions correct about general dentistry. Dentists answered 26.6% ± 20.5% of the questions correct about possible oral manifestations of gastrointestinal diseases and 50.3% ± 18.7% of the questions correct about gastrointestinal diseases. Gastroenterologists and dentists valued interdisciplinary consultation as very useful with scores of 4.07 ± 0.70 and 4.67 ± 0.49 on a 5-point Likert scale, respectively, but the frequency of consultation was considered insufficiently with a mean score of 2.88 ± 1.01 and 2.24 ± 1.05 on a 5-point Likert scale, respectively. Conclusions This study suggests that the knowledge of gastroenterologists and dentists about gastrointestinal diseases with oral manifestations could be improved. Interdisciplinary consultation was considered valuable for the optimal treatment of their patients but was assessed as insufficient.