The molecular dynamics in a variety of poly(ethylene isophthalate)s (PEIs) is studied by broadband dielectric spectroscopy (BDS). The materials comprise non-substituted main chain polyesters and polyesters with semifluorinated (oxydecylperfluorodecyl) side chains. Combining temperature-dependent small angle X-ray scattering (T-SAXS), differential scanning calorimetry (DSC) and BDS it can be shown that the microphase separated semifluorinated polymers exhibit independent dynamic glass transition relaxations taking place in the separate microphases. Additionally in the glassy state, the non-substituted polymers show an Arrhenius-type relaxation whose activation energy decreases gradually from 52 to 40 kJ/mol with increasing main chain flexibility. The sernifluorinated polymers exhibit a relaxation assigned to fluctuations of the perpendicular component of the fluoroalkyl end group with activation energies between 38 and 40 kJ/mol. With increasing flexibility of the main chain, the dynamics of the backbone becomes faster for the non-substituted polymers while an opposite trend is observed in the oxydecylperfluorodecyl substituted side-chain materials. A detailed explanation of the molecular origin of the relaxations is provided. (c) 2006 Elsevier Ltd. All rights reserved.