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BACKGROUND The traditional view considers that Chenpi (dried citrus peel) stored over the long-term has better health efficacies compared to fresh Chenpi, although the detailed mechanism responsible for this remains obscure. RESULTS The three water-soluble pectic polysaccharides (CPP1, CPP5 and CPP10) were obtained from 1-, 5- and 10-year Chenpi, respectively, and their physicochemical characteristics and intestinal immunomodulating activities were investigated and compared. The results obtained showed that CPP5 and CPP10 demonstrated a lower dynamic viscosity and degree of methylesterification, as well as a higher molecular heterogeneity, compared to CPP1. Monosaccharide composition analysis indicated that CPP1 was composed of arabinose, galacturonic acid and galactose, and a small amount of rhamnose; however, CPP5 and CPP10 consisted of arabinose, galacturonic acid, galactose, glucose and xylose, and a small amount of rhamnose. With the extension of storage period of Chenpi, the content of soluble conjugate phenolic acids increased in the pectic polysaccharide. Furthermore, it was confirmed that the pectic polysaccharides extracted from the 5-year and 10-year Chenpi could significantly enhance the proliferation of bone marrow cells via activating the Peyer's patch cells in vitro. CONCLUSION The present study demonstrates the differences in the pectic polysaccharides from Chenpi with different storage periods and also confirms that the pectic polysaccharides extracted from Chenpi stored over the long-term had more significant intestinal activities compared to that obtained from the fresh Chenpi. This phenomenon might partly explain why the Chenpi stored over the long-term has better healthcare effects. © 2018 Society of Chemical Industry.