To improve the extractability of carnosine and the levels of pro-oxidants such as iron in eel (Anguilla japonica) extracts, we examined the effects of extraction time, temperature, ion exchange chromatography and ultrafiltration (UF). The respective protein and total iron were reduced approximately 55 and 60% at 60$^{circ}C$, 63 and 70% at 80$^{circ}C$, 68 and 76% at 100$^{circ}C$ and 82 and 48% with ion exchange chromatography, respectively, compared to the untreated extract. However, there was no significant difference in the carnosine levels in the eel extracts. Ultrafiltration reduced the protein content of the extract by 52% compared with the untreated extract. UF reduced the protein contents of the samples from 60, 80, and 100% heat treatment and ion exchange chromatography treatment by 27, 50, 46 and 47%, respectively. UF reduced the total iron contents of the identical four treatments by 14, 22, 23, and 43%, respectively, while UF increased the carnosine by 23, 17, 20, and 6%, respectively.