Abstract Dysphagia is a common adverse effect of fundoplication and in some patients, there is no clear identifiable cause despite extensive investigation. Subtle anatomical features of anti-reflux surgery may relate to dysphagia. In this study multiple observers examine gastro-esophageal junction (GEJ) anatomy using objective measures of video-fluoroscopy swallow study (VFSS) to explore possible correlates with post-fundoplication dysphagia. Methods Thirty-one patients underwent structured VFSS 6–12 months after laparoscopic total (TotLF) or partial anterior (PAntLF) fundoplication recording: standing AP, 2x standing oblique (SOb), 2x prone oblique (POb), and prone oblique with continuous drinking (PObCont). Post-operative dysphagia was evaluated (Dakkak & Bennett Score: range 0–45; troublesome ≥12). Three observers (Obs1–3) independently measured: GEJ displacement anteriorly; degree of axis deviation of esophagus & GEJ (E-GEJ); posterior distal esophageal angle (PDEA); and GEJ opening diameter cf. maximal distal esophageal diameter (ME-GEJ). Correlations between measurements and dysphagia by operation type were assessed using linear regression analysis and linear mixed-effects models. Results Post-operatively, 5/18 TotLF and 4/13 PAntLF patients reported troublesome dysphagia. Three observers independently found: patients with troublesome dysphagia after TotLF had greater anterior displacement of the GEJ (SOb, range 0.61 cm–1.18 cm, Obs1 p = 0.04), and larger axis deviation of E-GEJ (POb, range 3.28°-13.07°, Obs2 p = 0.03) compared to patients with no/mild dysphagia. There was a trend for greater PDEA in patients with troublesome dysphagia after TotLF (POb, range 0.46°-2.12° and PObCont, range 3.37°-13.4°), but this trend did not reach statistical significance. Following PAntLF, all observers recorded a reduction in ME-GEJ for each unit of worsening dysphagia (PObCont, range 0.03 cm–0.04 cm, Obs1 p = 0.02, Obs2 p = 0.02). Conclusion Multiple observers concur that anterior GEJ displacement, the angle between the esophagus axis—GEJ axis, and posterior distal esophageal angulation are anatomical factors associated with troublesome dysphagia after total fundoplication. After partial anterior fundoplication, a small reduction in GEJ opening diameter relative to the distal esophagus related to worsening dysphagia. To reduce post-fundoplication dysphagia, attention to operative techniques affecting angulation and luminal diameter at the GEJ by fundoplication and hiatal repair is warranted.