In plants and fungi, sphingolipids, characterized by the presence of a sphingoid base (SB), comprise neutral classes, including ceramide (Cer) and glucosylceramide (GlcCer), and acidic classes, including glycosyl inositol phosphoryl ceramide (GIPC). The major class of plant and fungal sphingolipids is GIPC; however, owing to their complicated extraction and analysis, there is still little information regarding the food characteristics of GIPC compounds. In the present study, we evaluated the content and SB composition of highly polar sphingolipids (HPS) in materials that had been obtained from our previous food processing study for GlcCer and Cer. This assessment was based on the changes that occur in HPS containing GIPC in sake rice (saka-mai) during the rice polishing and sake (rice wine) brewing process. In addition, we report a new investigation into the composition of sphingolipids in koji rice and sake yeast. HPS levels were the highest among the sphingolipid classes in brown rice cultivars and highly polished rice. Sake and sake lees (sake-kasu) were produced using three different starter cultures. In sake lees, Cer levels were the highest among the classes, while HPS was greatly reduced based on the amount of highly polished rice and koji rice, and these HPS were mainly composed of sphinganine (d18:0), which is a minor SB in highly polished rice, koji rice, and sake yeast. In addition, considerable levels of free SBs, mainly comprising d18:0, were detected in sake lees. The levels of HPS and free SBs in sake lees were dependent on the starter culture. These results suggest that HPS was hydrolyzed to Cer and that sake yeast also affected the levels of Cer and free SBs during brewing. One interesting question raised by these results is whether changes in the class and base compositions of sphingolipids during brewing contribute to taste of the final product and other food functions.