Background: The aim of this study was to investigate if the flattening filter free (FFF) irradiation mode of a linear accelerator (linac) is advantageous as compared to the flat beam (FF) irradiation mode in intensity modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT) for carcinoma of the hypopharynx/larynx. Methods: Four treatment plans were created for each of 10 patients for an Elekta Synergy linac with Agility collimating device, a dual arc VMAT and a nine field step and shoot IMRT each with and without flattening filter. Plan quality was compared considering target coverage and dose to the organs at risk. All plans were verified by a 2D-ionization-chamber-array and delivery times were compared. Peripheral point doses were determined as a measure of second cancer risk. The Wilcoxon test was used for statistical analysis with a significance level of 0.05. Results: Plan quality was similar for all four treatment plans without statistically significant differences of clinical relevance. The clinical goals were met in all plans for the PTV-SIB (V-95% > 95%), the spinal cord (D1ccm < 45 Gy) and the brain stem (D-1ccm < 48 Gy). For the parotids, the goal of D-50% < 30 Gy was met in 70% and 60% of the plans for the left and right parotid respectively, and the V-95% of the SIB reached an average of 94%. Delivery times were similar for FF and FFF and significantly decreased by around 70% for VMAT as compared to IMRT. Peripheral doses were significantly reduced by 18% in FFF mode as compared to FF and by 26% for VMAT as compared to IMRT. Lowest peripheral doses were found for VMAT FFF, followed by VMAT FF. Conclusions: The FFF mode of a linear accelerator is advantageous for the treatment of hypopharynx/ larynx carcinoma only with respect to reduction of second cancer induction in peripheral organs for the combination of Elekta Synergy linacs and Oncentra (R) External Beam v4.5 treatment planning system. This might be of interest in a therapy with curative intent.