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Purpose: The aim of this study was to implement a protocol for reference dosimetry in tomotherapy and to validate the beam output measurements with an independent dosimetry system. Methods: Beam output was measured at the reference depth of 10 cm in water for the following three cases: (1) a 5 x 10 cm(2) static machine specific reference field (MSR), (2) a rotational 5 x 10 cm(2) field without modulation and no tabletop in the beam, (3) a plan class specific reference (PCSR) field defined as a rotational homogeneous dose delivery to a cylindrical shaped target volume: plan with modulation and table-top movement. The formalism for reference dosimetry of small and nonstandard fields [Med.Phys. 35: 5179-5186, 2008] and QA recommendations [Med.Phys. 37: 4817-4853, 2010] were adopted in the dose measurement protocol. All ionization chamber measurements were verified independently using alanine/EPR dosimetry. As a pilot study, the beam output was measured on tomotherapy Hi-art systems at three other centers and directly compared to the centers specifications and to alanine dosimetry. Results: For the four centers, the mean static output at a depth of 10 cm in water and SAD = 85 cm, measured with an A1SL chamber following the TG-148 report was 6.238 Gy/min +/- 0.058 (1 SD); the rotational output was 6.255 Gy/min +/- 0.069 (1 SD). The dose stated by the center was found in good agreement with the measurements of the visiting team: D(center)/D(visit) = 1.000 +/- 0.003 (1 SD). The A1SL chamber measurements were all in good agreement with Alanine/EPR dosimetry. Going from the static reference field to the rotational/non modulated field the dose rate remains constant within 0.2% except for one center where a deviation of 1.3% was detected. Conclusions: Following the TG-148 report, beam output measurements in water at the reference depth using a local protocol, as developed at different centers, was verified. The measurements were found in good agreement with alanine/EPR dosimet