We apply extensive molecular dynamics simulations and analytical considerations in order to study the conformations and the effective interactions between weakly charged, flexible polyelectrolyte chains in salt-free conditions. We focus on charging fractions lying below 20%, for which case there is no Manning condensation of counterions and the latter can be thus partitioned in two states: those that are trapped within the region of the flexible chain and the ones that are free in the solution. We examine the partition of counterions in these two states, the chain sizes and the monomer distributions for various chain lengths, finding that the monomer density follows a Gaussian shape. We calculate the effective interaction between the centers of mass of two interacting chains, under the assumption that the chains can be modeled as two overlapping Gaussian charge profiles. The analytical calculations are compared with measurements from molecular dynamics simulations. Good quantitative agreement is found for charging fractions below 10%, where the chains assume coil-like configurations, whereas deviations develop for charge fraction of 20%, in which case a conformational transition of the chain towards a rodlike configuration starts to take place. (C) 2004 American Institute of Physics.