Although the sensitive detection of putaminal iron deposition by T2*-weighted imaging (T2*-WI) is of diagnostic value for multiple system atrophy (MSA), the diagnostic significance of the pontine hot-cross bun (HCB) sign with increased ferritin-bound iron in the background remains unknown. We retrospectively evaluated the cases of 33 patients with cerebellar-form MSA (MSA-C) and 21 with MSA of the parkinsonian form (MSA-P) who underwent an MRI study with a 1.5-T system. Visualization of the HCB sign, posterior putaminal hypointensity and putaminal hyperintense rim on T2*-WI was assessed by two neurologists independently using an established visual grade, and were compared with those on T2-weighted imaging (T2-WI). The visual grade of pontine and putaminal signal changes was separately assessed for probable MSA (advanced stage) and possible MSA (early stage). T2*-WI demonstrated significantly higher grades of HCB sign than T2-WI (probable MSA-C, n = 27, p < 0.001; possible MSA-C, n = 6, p < 0.05; probable MSA-P, n = 13, p < 0.01). The visual grade of the HCB sign on T2*-WI in the possible MSA-C patients was comparable to that in the probable MSA-C patients. Although the HCB sign in MSA-P was of lower visual grade than in MSA-C even on T2*-WI, some patients showed evolution of the HCB sign preceding the appearance of the putaminal changes. These findings suggest that T2*-WI is of extreme value for detecting the HCB sign, which is often cited as a hallmark of MSA. The appearance of the HCB sign on T2*-WI might not only support but also improve the diagnosis of MSA.