The endogenous dipeptides, carnosine and related compounds, are the naturally occurring dipeptides with multiple neuroprotective properties. We have examined the protective effects of carnosine, homocarnosine and anserine on the aggregation of neurofilament-L (NF-L) induced by neurotoxin, acrolein. When NF-L was incubated with acrolein in the presence of carnosine, homocarnosine or anserine, protein aggregation was inhibited in a concentration-dependent manner. These compounds inhibited the formation of protein carbonyl compounds and dityrosine in acrolein-mediated NF-L aggregates. The aggregates of NF-L displayed thioflavin T reactivity, reminiscent of amyloid. This thioflavin T reactivity was inhibited by carnosine and related compounds. This effect was associated with decreased formation of oxidatively modified proteins. Our results suggested that carnosine and related compounds might have protective effects to brain proteins under pathophysiological conditions leading to degenerative damage such as neurodegenerative disorders.