During the synthesis of ZnSe nanowires various point and extended defects can form, leading to observed stacking faults and twinning defects, and strong defect related emission in photoluminescence spectra. In this paper, we report on the development of a simple thermodynamic model for estimating the defect concentration in ZnSe nanowires grown under varying Se vapour pressure and for explaining the results of our experimental findings. Positron annihilation spectroscopy was used successfully for the first time for nanowires and the results support predictions from the defect model as well as agreeing well with our structural and optical characterization results. Under very high Se vapour pressure, Se nodules were observed to form on the sidewalls of the nanowire, indicating that beyond a limit, excess Se will begin to precipitate out of the liquid alloy droplet in the vapour-liquid-solid growth of nanowires.