The study analysed the stability of polyphenols present in extracts isolated from cocoa, green tea and strawberries in Hank’s Balanced Salt Solution buffers. The extracts were incubated under conditions commonly used for intestinal absorption experiments with human epithelial cells. The polyphenols were analysed with HPLC-MS method. The concentrations of most of the polyphenols monitored changed during 2 h of incubation. The flavan-3-ols of cocoa exhibited similar stability and all were more stable at pH 6.5 than 7.4. The concentration of procyanidin B2 at pH 7.4 decreased to the highest extent. Green tea predominant catechins: epigallocatechin gallate and epigallocatechin, were very vulnerable in HBSS both at pH 6.5 and 7.4; their specific molecular structure may be responsible for this phenomenon. The anthocyanins of a strawberry extract were more stable at pH 6.5. The considerable increase in ellagic acid concentration at pH 7.4 might be explained by possible degradation of other compounds of the extract. It is highly recommended to perform stability tests before transport experiments in a cell culture model in order to avoid misinterpretation of results.