The early stages of combustion are considered for a flame viewed as a site for in situ chemical ionization. This study explores the information provided by the measurement of axial concentration profiles for both positive and negative ion species upstream in a conical premixed methane-oxygen flame of fuel-lean composition (equivalence ratio = 0.2) burning at atmospheric pressure. Making use of existing energetic and kinetic data now available for individual ion-molecule reactions, the profile information can be interpreted to reveal the mechanisms which dominate the positive and the negative ion chemistry independently. Confidence in these general mechanisms leads in turn to interpretation of the nature and behaviour of the underlying neutral species present upstream in the flame. A neutral beam sampling study of a similar flame is available in the literature for comparison purposes, and our work corroborates the presence of a number of neutral species (O 2, H 2O, CO, CO 2, O, OH, HO 2, HCHO, CH 3OH, CH 3O 2). Initiated by the protons available from primary CHO + ions, the positive ion chemistry is dominated by fast proton transfer reactions which indicate the presence of other neutrals in protonated form (CH, CH 2, CH 3, C 2H 2, HCO, CH 3CHO, CH 2CO, CH 3CHCO and possibly C, HCOOH, C 2H 5CHO). The negative ion chemistry is more complicated, involving charge transfer, proton transfer and rearrangement with an uncertain contribution from three-body association reactions and switching reactions. Nevertheless, the negative ion data indicate the presence of several neutral species not previously reported for this fuel-lean flame (C 2H 2, CH 2CO, O 3 with inconclusive evidence for HCOOH).