Loss mechanisms in 1-10 kW spark-ignition, two-stroke engines may be grouped into five categories: thermal losses, frictional losses, sensible enthalpy in the exhaust gases, incomplete combustion, and short-circuiting of fresh fuel and air mixture. These loss mechanisms cause small two-stroke engines to have fuel conversion efficiencies 50%-70% lower than similar larger engines. Previous studies of loss scaling in small engines have estimated the short-circuiting using heuristics derived for larger engines or grouped it with other combustion losses to complete the energy balance. This work describes and compares two methods for measuring short-circuiting on a commercially available, two-stroke, naturally aspirated, spark ignition engine with 55 cm3 displacement. One method used oxygen as an analyte (the Watson method), nitrogen as an internal standard, and gas chromatography with a thermal conductivity detector for quantification. While the Watson method is historically proven, it only works under globally rich combustion conditions. The other method, selected for its potential to work under lean combustion conditions, used iso-octane as an analyte, argon as an internal standard, and gas chromatography for separation with mass spectrometry for identification and quantification. The iso-octane method yielded results within 4% of the Watson method, a difference that is statistically indistinguishable at the 95% confidence level. Therefore, despite the larger uncertainty of the iso-octane method (10%-15% versus 3%-5% for Watson's method), the iso-octane method offers a valid method for determining short-circuiting under lean combustion conditions.