Objective JNK signaling pathway regulates some physiological activities, including inflammation, cell proliferation, differentiation, apoptosis and stress response. The study was to compare the role of JNK signaling pathway in rat liver regeneration (LR) and in rat liver cirrhosis (LC) at the gene transcription level.Methods The rat LR model was established by 2/3 partial hepatectomy(PH), and the LC model was induced by intraperitoneal injection of CClSUB>4/SUB> and colza oil. Rat Genome 230 2.0 array was used to detect gene expression profiles of JNK signaling pathway-related genes , and bioinformatics and systems biology methods were used to analyze the physical activities which were predicted by the expression profiles.Results JNK signaling pathway includes 302 genes and 42 branches. Of them, 240 genes were contained in Rat Genome 230 2.0 array, including 79 significantly expressed genes. In detail, 52 genes were the LR-specific, 5 genes the LC-specific, and 22 genes the common. The cell proliferation-promoting effect of paths 1 and 16 and the cell apoptosis-promoting effect of paths 22-33 became stronger at the priming phase of LR than in control; the cell proliferation-promoting effect of paths 1-17, 34 and 35 and cell apoptosis-promoting effect of paths 22-33 was enhanced at the progressing phase of LR, while the cell apoptosis-inhibiting effect of paths 37-41 and the cell apoptosis-inducing effect of paths 37, 39, 41 and 42 was weakened at the terminal phase. Paths 18-21 and 36 were found not to be involved in rat LR. JNK signaling pathway of LC worked as that of the control did. Conclusion Thirty-seven branches of the JNK signaling pathway regulat cell proliferation and apoptosis in rat LR, but may not be significantly involved in rat LC.