BACKGROUND Oesophageal motility classification using high resolution manometry (HRM) has been established in the supine position. Nevertheless, examination in the sitting position is more physiological. Our aim was to determine if body position modifies oesophago-gastric junction (OGJ) morphology and oesophageal motility. METHODS A total of 100 patients (47 males, mean age 51 years) were included in this study. The oesophageal HRM protocol included examination in supine and sitting positions. Recordings were reviewed by two different operators. Amplitude, duration, velocity, Distal Contractile Integral (DCI) and Pressurization Front Velocity of oesophageal waves induced by swallowing were recorded. KEY RESULTS The lower oesophageal sphincter resting pressure was not significantly changed by body position. The sitting position modified the OGJ classification in 12 patients. The inter-observer agreement to classify OGJ was moderate (kappa = 0.54 and 0.46, in the supine and sitting positions respectively) while it was good to diagnose motility disorders (kappa = 0.72 and 0.83). The percentage of normal waves was lower in the sitting position in comparison with the supine position (56%vs 67%, P < 0.01). The DCI was also lower in the sitting position (1125 mmHg.s.cm vs 1639, P < 0.01) as well as the amplitude of oesophageal waves. Finally the diagnosis was concordant in both positions in 72 patients. CONCLUSIONS & INFERENCES Body position can affect OGJ morphology and oesophageal motility assessment by HRM in some patients. Normal values in the sitting position should thus be determined. Inter-observer variation for the proposed classification of OGJ morphology must also be taken into account.