Colon cancer is one of the major causes of cancer mortality worldwide. The analysed feeds, containing non-genetically modified (GM) soybean and Roundup Ready soybean, showed a different polyphenolic content and lipophilic composition. Non-GM soybean extract possessed twice the polyphenolic content of GM soybean and the highest number of sterols. Among them, γ-sitosterol was found to be the major constituent. Methanolic extract of non-GM soybean extract was more potent than GM soybean extract against colon carcinoma cell line LoVo using MTT assay, while the second one showed a slightly higher anti-inflammatory activity. The findings add to epidemiological evidence for the therapeutic effects of soy foods in colorectal carcinoma.