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Long T2 water contamination is a major challenge with direct in vivo UTE imaging of ultrashort T2 components in the brain since water contributes most of the signal detected from white and gray matter. The Short TR Adiabatic Inversion Recovery prepared Ultrashort TE (STAIR-UTE) sequence can significantly suppress water signals and simultaneously image ultrashort T2 components. However, the TR used may not be sufficiently short to allow the STAIR preparation to completely suppress all the water signals in the brain due to specific absorption rate (SAR) limitations on clinical MR scanners. In this study, we describe a STAIR prepared dual-echo UTE sequence with complex Echo Subtraction (STAIR-dUTE-ES) which improves water suppression for selective ultrashort T2 imaging compared with that achieved with the STAIR-UTE sequence. Numerical simulations showed that the STAIR-dUTE-ES technique can effectively suppress water signals and allow accurate quantification of ultrashort T2 protons. Volunteer and Multiple Sclerosis (MS) patient studies demonstrated the feasibility of the STAIR-dUTE-ES technique for selective imaging and quantification of ultrashort T2 components in vivo. A significantly lower mean UltraShort T2 Proton Fraction (USPF) was found in lesions in MS patients (5.7 ± 0.7%) compared with that in normal white matter of healthy volunteers (8.9 ± 0.6%). The STAIR-dUTE-ES sequence provides robust water suppression for volumetric imaging and quantitation of ultrashort T2 component. The reduced USPF in MS lesions shows the clinical potential of the sequence for diagnosis and monitoring treatment in MS.