A helicon plasma etch reactor is simulated using direct simulation Monte Carlo and particle-in-cell methods for a chlorine (Cl-2) feed gas flow. Computations for the gas discharge are carried out by modeling the ions and neutrals as particles and by imposing the electrons as a background condition conforming to experimental measurements. The neutrals and ions are then allowed to interact with the background electrons and to relax to a steady state. The effects on the reactor flow field and etch rate of chlorine atom recombination into chlorine molecules at the walls is investigated. Results show that recombination at the walls results in the depletion of the amount of chlorine atoms (Cl) in the reactor. The depleted chlorine atom population leads to lower ionization levels and a diminished ion (Cl+) flux to the wafer. Consequently, the etch rate is decreased by as much as 15% when compared to simulations without recombination. The creation of chlorine (Cl-2) molecules at the walls through recombination also provides a new source for negative ions (Cl-) which increases the electronegativity of the plasma. In addition, the results of the simulation are compared with ion current and optical emission spectroscopy (OES) measurements. The Cl-Ar ratio (measured by the OES technique) increases less than 20% from the centerline to the wall of the reactor. An inspection of absolute densities, however, reveals that the individual near-wall densities are as much as a factor of 2 greater than the centerline densities. The trace species, Ar, therefore, does not become distributed evenly throughout the reactor.