Purpose β(1,3)/(1,6)-Glucan of yeast origin is a bioactive polysaccharide used in nutrition, healthcare, agriculture and wastewater treatment. Yeast cultivation focused on the biosynthesis of β-glucan with simultaneous utilization of industrial wastes as a culture medium is a new way of obtaining these functional polysaccharides. The aim of current study was to isolate and characterize the purified β(1,3)/(1,6)-glucan preparation from Candida utilis ATTC 9950 biomass propagated in waste deproteinated potato juice water with the addition of glycerol. Methods The production of biomass of tested C. utilis strain was carried on biofermentor scale. The isolation of cell wall β-glucan was tested with two different methods: the alkaline-acid procedure coupled with hot-water extraction (method 1) and isolation based on cell wall autoclaving, lipids extraction and proteolysis (method 2). The isolated fractions were further analyzed with infrared spectroscopy. Results Obtained preparations contained approx. 82% of β(1,3)/(1,6)-glucan after shortened extraction comparing with procedures described in literature. Infrared spectra of examined preparations demonstrated highly similar pattern to β-glucan standard of Saccharomyces cerevisiae origin. The preparation produced by method 2 showed higher ratio of β(1,3)-to β(1,6)-glucan. The production efficiency for method 2 was 70%, while for the method 1 it was significantly lower, i.e. 49%, indicating substantial material losses during alkaline-acid purification. Conclusions The C. utilis ATCC 9950 yeast cultivated on waste deproteinated potato juice water supplemented with glycerol is a highly efficient system to obtain purified β-glucan preparation.