OBJECTIVES: The aim of the study was to investigate whether the type of instrumental swallowing examination (Fibreoptic Endoscopic Evaluation of Swallowing (FEES) or videofluoroscopy) influences perception of post-swallow pharyngeal residue. DESIGN: Prospective, single-blind assessment of residue from simultaneous videofluoroscopy and FEES recordings. All raters were blind to participant details, to the pairing of the videofluoroscopy and FEES examinations and to the other raters' scores. SETTING: Tertiary specialist ENT teaching hospital. PARTICIPANTS: Fifteen adult participants consecutively recruited; seven women and eight men aged between 22 and 73, mean age 53. All participants underwent one FEES examination and one videofluoroscopy examination performed simultaneously. INCLUSION CRITERIA: referred to speech and language therapy for assessment of dysphagia. EXCLUSION CRITERIA: nil by mouth or judged to be at high risk of aspiration. MAIN OUTCOME MEASURES: The FEES and videofluoroscopy examinations were recorded simultaneously. Fifteen speech and language therapists independently scored pharyngeal residue as none, coating, mild, moderate or severe. All examinations were scored twice by all raters. RESULTS: Intra- and inter-rater agreement were similar for both examinations. There were significant differences between FEES and videofluoroscopy pharyngeal residue severity scores (anova, P < 0.001). FEES residue scores were consistently higher than videofluoroscopy residue scores. CONCLUSIONS: Pharyngeal residue was consistently perceived to be greater from FEES than from videofluoroscopy. These findings have significant clinical implications as FEES and videofluoroscopy findings are used to judge aspiration risk and to make recommendations for oral intake. Further research is required to examine the impact of FEES and videofluoroscopy examinations on treatment decisions.