Three series of segmented poly(ester urethanes) containing poly(caprolactodiols) as flexible segments were synthesized. Polymers of series I were devoid of side chains, polymers of series II contained side chains at rigid segments, while in the polymers of the third series, side chains were attached to flexible segments. The rigid segments in the polymers of series I and II were derived from 2,4- and 2,6-toluylene diisocyanate (80:20) and 1,4-butanediol, and the polymers of series III were prepared from 2,4- and 2,6-toluylene diisocyanate and glycerol monooleate. It was discovered that the location of side chains representing the residues of oleic acid and the molecular mass of the flexible segment affect the Tg, Tm, degree of crystallinity, packing coefficient, ultimate tensile strength, and elongation at break of the synthesized poly(ester urethanes). It was shown that the location of side chains does not influence the extent of the microphase separation of flexible and rigid segments of poly(ester urethanes) based on poly(caprolactodiols). Side chains located at flexible segments deteriorate the order of polymer structure to a higher extent than do side chains attached to a rigid segment.