Density functional calculations within the Car-Parrinello framework are used to obtain self-consistently the electronic and the geometrical structures of polythiophene derivatives. The relation between the electronic states and quinoid vs aromatic structures is studied on a series of substituted polythiophenes (PTh) and polyisothianaphthenes (PITN), Excellent agreement is found with experimental data, where these are available. Some shortcomings of semiempirical methods in describing pi bonds with heteroatoms are revealed, A unique minimal energy structure is obtained for each of the polymers; no other local minima are found, The general rule is that a polymer adapts the structure that leads to the largest possible band gap, which for PTh-like polymers is the aromatic structure and for PITN-like polymers is the quinoid structure. Substitutions do not change the basic geometry and electronic structure of either PTh or PITN but can alter the band gap by several tenths of an electronvolt.