This study characterized the blood oxygen level-dependent (BOLD) fluctuations in benign and malignant musculoskeletal tumours via power spectrum analyses in pre-established low-frequency bands. BOLD MRI and T1-weighted imaging (T1WI) were collected for 52 patients with musculoskeletal tumours. Three ROIs were drawn on the T1WI image in the tumours’ central regions, peripheral regions and neighbouring tissue. The power spectrum of the BOLD within each ROI was calculated and divided into the following four frequency bands: 0.01–0.027 Hz, 0.027–0.073 Hz, 0.073–0.198 Hz, and 0.198–0.25 Hz. ANOVA was conducted for each frequency band with the following two factors: the location of the region of interest (LoR, three levels: tumour “centre”, “peripheral” and “healthy tissue”) and tumour characteristic (TC, two levels: “malignant” and “benign”). There was a significant main effect of LoR in the frequencies of 0.073–0.198 Hz and 0.198–0.25 Hz. These data were further processed with post-hoc pair-wise comparisons. BOLD fluctuations at 0.073–0.198 Hz were stronger in the peripheral than central regions of the malignant tumours; however, no such difference was observed for the benign tumours. Our findings provide evidence that the BOLD signal fluctuates with spatial heterogeneity in malignant musculoskeletal tumours at the frequency band of 0.073–0.198 Hz
