This study aimed to elucidate the mechanism of dysphagia by determining the simultaneous relationships between subjective perception of swallow with oesophageal motility and bolus transport in patients with non-obstructive dysphagia (NOD). Combined oesophageal manometry and impedance was performed in 18 consecutive NOD patients and 14 healthy controls. Swallow was abnormal if the amplitude of distal oesophageal contractions was less than 30 mmHg or simultaneous contractions occurred. Bolus transit was abnormal if bolus exit was not found at one or more of the measuring sites. Perception of each swallow was assessed using a standardized scoring system and was enhanced if score was >1. The prevalence of complete bolus transit was lower in NOD patients compared with healthy controls (P= 0.001). Abnormal liquid bolus transit was found in 40% of patients with normal motility and 38% of patients with abnormal motility, whereas abnormal viscous bolus transit was observed in 38% of patients with normal motility and 70% of patients with abnormal motility. Agreement between enhanced perception and impedance was poor during liquid (κ = 0.12, 95% CI: −0.003 to 0.233) and viscous swallowing (κ = 0.12, 95% CI: −0.004 to 0.244). Agreement between enhanced perception and manometry was even poorer during liquid (κ = −0.16, 95% CI: −0.302 to 0.022) and viscous swallowing (κ = −0.12, 95% CI: −0.25 to 0.002). NOD patients show poor correlation between dysphagia and oesophageal motility parameters. The results suggest that, in patients with NOD, oesophageal motor dysfunction may play a limited role, if any, in the generation of dysphagia.