Rice prolamin, constituting type-I protein body (PB-I), is indigestible and causes deterioration of rice protein nutritional quality. In this study, the in vivo digestibility of rice protein isolates was investigated by tracing their intraluminal transit in the gastrointestinal (GI) tract of rats by western blotting and by observing the structures excreted in the feces by electron microscopy. Two types of rice protein isolates, produced by alkali extraction (AE-RP) and by starch degradation (SD-RP), were compared. The protein patterns in the isolates were similar, but their digestion in the GI-tract showed striking differences. In the AE-RP group, 13-kDa prolamin (13P) quickly disappeared in the lower GI tract and was not excreted in the feces. By contrast, in the SD-RP group, 13P accumulated massively and nearly intact PB-Is were excreted. These results indicate that the in vivo digestibility of prolamin can be improved by alkali extraction through structural changes to it.