Due to the excellent physicochemical and biomedical properties, silk fibroin (SF) is a good source for the development of biomedical materials, where size selection of SF during biological application heavily affects the related biomedical behaviors. In this research, silk fibroin was step-wisely filtered and classified by syringe filter into four particle sizes ranges (< 200 nm, 200-450 nm, 450-800 nm and > 800 nm), and was then labeled with iodine-125 (125I-SF) for nuclear imaging. Super early (0-40 minutes) and primary (1-72 hours) biodistribution of 125I-SF were evaluated in Wistar rats. SEM-proved spherical or irregular silk fibroin powder with mixed size was not reuniting with each other in aqueous solution. For early in vivo distribution, four SF mostly gathered in the gastrointestinal tract (120-140 times to the background (accumulation in upper limb of left hind leg)), and a small amount (20-40 times) in bladder after injection within 40 min. For SF (< 200 nm, 200-450 nm and 450-800 nm) during the first 72 h, although there was decreasing trend over time, the gastrointestinal accumulation still accounted for the majority. Meanwhile, most of the SF in the bladder was expelled within 1 h and SF could be rarely seen in liver. Notably, SF (> 800 nm) almost gathered in the liver instead of the gastrointestinal tract after 10 h and got the peak value (280 times to the background) at around 48 h. The particle size directly determined the passive distribution of SF in vivo, which can not be ignored during drug design. Above all, these preliminary results may be referable for further biomedical application on silk fibroin.