The effect of the chemical-composition heterogeneity of flexible-chain binary copolymers on their separation in size-exclusion chromatography (SEC) was theoretically examined. The two parameter theory of polymer solutions was engaged to estimate the coil size. The variation in molecular weight is shown for copolymer molecules which differ in the ratio of the two constituent monomeric units but have the same coil size and, therefore, are eluted at the same elution volume. The result was applied to a theoretical case of analysis of copolymers, the composition and molecular-weight distributions of which are given by theoretical functions. If the refractive index increments of homopolymers whose units constitute the copolymer are equal or close to each other, the influence of the chemical heterogeneity on the experimental data is below the experimentally detectable limit. A significant error in the determination of the molecular-weight averages can occur only if the difference in the refractive index increments exceeds physically reasonable limits.