Apolipoprotein E (ApoE) is strongly associated with late-onset familial and sporadic forms of Alzheimer's disease. Some myopathic changes which are similar to those seen in Alzheimer brain, that is, deposits of βAP and tau protein, could be induced by chronic intoxication with chloroquine. The influence of chloroquine treatment on ApoE expression in rat muscle was examined using reverse transcription followed by polymerase chain reaction (RT-PCR). A steadily expressed endogenous mRNA, glyceradehyde-3-phosphate dehydrogenase (G3PD) was served as an internal standard in PCR quantification. Amplification was found to be linear over a wide range of cycle number, and the efficiency was identical for target and control mRNA in RT-PCR. The expression of ApoE mRNA in rat muscle began to increase after 6 weeks of chloroquine treatment, and became 20-fold more than that in untreated control later on. The results suggest that ApoE may play roles in the pathologic changes in rat muscle caused by chronic intoxication with chloroquine.