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There is a great demand of salt-tolerant sugarcane planting material in Cuba. Temporary immersion bioreactors (TIB) are effective to significantly increase sugarcane in vitro shoot proliferation rate from 1:4 in conventional containers to about 1:35. Sugarcane micropropagation in TIBs under NaCl stress may help screen mutants with salinity tolerance. We developed the experiment shown here to identify a NaCl concentration able to stress shoot in TIBs. At 30 days of culture initiation with different NaCl levels (0 - 200 mM), explant multiplication rate, shoot cluster fresh mass, and levels of aldehydes, chlorophylls, carotenoids and phenolics were determined in the plant material. Content of soluble phenolics in the culture medium was also evaluated. Addition of NaCl decreased shoot multiplication rate and fresh mass. Other statistically significant differences were recorded but the most important were noted in the increased contents of carotenoids, malondialdehyde, other aldehydes and soluble phenolics in the plants, and in the soluble phenolics in the culture medium. This research may be useful for future experiments of in vitro selection of new sugarcane genetic materials with NaCl tolerance. Fifty percent of multiplication rate was reduced with 89 mM NaCl which can be used to stress shoots during micropropagation in TIBs and eventually detect mutants with salt tolerance. © The Author(s) 2017.