BACKGROUND: Pectin characteristics from different parts of lemon fruit (Citrus limon L.) were studied as a basis for assessing their suitability for functional applications. Pectin was extracted from lemon albedo, lemon core parts and membranes, and lemon extract using an aqueous extraction protocol. The composition and structural properties of the isolated pectins were examined by means of complementary analytical methods to assess their molecular characteristics for potential industrial applications. RESULTS: The isolation protocol yielded pectins that were predominantly composed of galacturonic acid, with differences in the degree of methylation and neutral sugars content, and with low protein content, indicating high-purity materials. The same extraction protocol resulted in differences in yield and purity between the three different parts of lemon fruit, and in structural variations in the pectin backbone, as evidenced by differences in sugar composition and molecular weight. Solutions of the isolated lemon pectins exhibited pseudoplastic behavior. Macromolecular characterization showed that the lemon extract pectin had the highest molecular weight and hydrodynamic volume, followed by lemon core and lemon albedo pectin. CONCLUSION: The work demonstrates that pectins with distinct structural properties may be extracted from different parts of lemon wastes and used for different technological purposes.