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Purpose: Recently, an international working group on nonstandard fields presented a new formalism for ionization chamber reference dosimetry of small and nonstandard fields [Alfonso et al., Med. Phys. 35, 5179-5186 (2008)] which has been adopted by AAPM TG-148. This work presents an experimental determination of the correction factors for reference dosimetry with an Exradin A1SL thimble ionization chamber in a TomoTherapy unit, focusing on: (i) machine-specific reference field, (ii) plan-class-specific reference field, and (iii) two clinical treatments., Methods: Ionization chamber measurements were performed in the TomoTherapy unit for intermediate (machine-specific and plan-class-specific) calibration fields, based on the reference conditions defined by AAPM TG-148, and two clinical treatments (lung and head-and-neck). Alanine reference dosimetry was employed to determine absorbed dose to water at the point of interest for the fields under investigation. The corresponding chamber correction factors were calculated from alanine to ionization chamber measurements ratios., Results: Two different methods of determining the beam quality correction factor k(Q,Q(0) ) for the A1SL ionization chamber in this TomoTherapy unit, where reference conditions for conventional beam quality determination cannot be met, result in consistent values. The observed values of overall correction factors obtained for intermediate and clinical fields are consistently around 0.98 with a typical expanded relative uncertainty of 2% (k = 2), which when considered make such correction factors compatible with unity. However, all of them are systematically lower than unity, which is shown to be significant when a hypothesis test assuming a t-student distribution is performed (p=1.8×10(-2)). Correction factors k(Q(clin),Q(pcsr) ) (f(clin),f(pcsr) ) and k(Q(clin),Q(msr) ) (f(clin),f(msr) ), which are needed for the computation of field factors for relative dosimetry of clinical beams, have been found to be very close to unity for two clinical treatments., Conclusions: The results indicate that the helical field deliveries in this study (including two clinical fields) do not introduce changes on the ion chamber correction factors for dosimetry. For those two specific clinical cases, ratios of chamber readings accurately represent field output factors. The values observed here for intermediate calibration fields are in agreement with previously published data based on alanine dosimetry but differ from values recently reported obtained via radiochromic dosimetry.