Abstract The formation of pollutant species in turbulent diffusion flames is strongly affected by the coupling between the highly non-linear chemical kinetics with three-dimensional, unsteady hydrodynamics. It is necessary to better understand this interdependency of transport and kinetic mechanisms, in order to accurately predict non-equilibrium effects in the numerical modeling of pollutant formation (especially PAH and soot). Unsteady counterflow diffusion flames can be conveniently used to address the effects of hydrodynamic unsteadiness on the pollutant chemistry, because they posses much of the physics postulated for diffusion flamelets and exhibit a large range of combustion conditions with respect to steady flames. Thus, these flames give insights into a variety of chemistry-flow field interactions important in turbulent combustion. In this paper, spatially resolved concentrations of PAH and soot are presented for counterflow diffusion flames fed with methane, propane and ethylene at several strain rates. Unsteady effects on the formation of PAH and soot are investigated for the propane flame by imposing harmonic oscillations in the strain rate with frequencies between 0.1 and 100 Hz. Numerical results reveal a net increase in the concentration of aromatic species and soot when the strain rate oscillations are imposed to the flame. The response of the flame in terms of soot and PAH concentrations appears strongly dependent on the applied forcing frequency. PAH and soot exhibit specific behavior according to their characteristic chemical time scales which are longer than those of the main combustion process. The PAH and soot formation is found more sensitive to velocity fluctuations for flames with large initial strain rate. At low frequencies of imposed oscillations the structure of the soot profile shows strong deviations from the steady-state profile. At large frequencies a decoupling between the soot concentration and the velocity field is evident.