Development of new fuels and engine combustion strategies for future ultra-low emission engines requires a greater level of insight into the process of emissions formation than is afforded by the approach of engine exhaust measurement. The paper describes the development of an in-cylinder gas sampling system consisting of a fast-acting, percussion-based, poppet-type sampling valve, and a heated dilution tunnel; and the deployment of the system in a single cylinder engine. A control system was also developed for the sampling valve to allow gas samples to be extracted from the engine cylinder during combustion, at any desired crank angle in the engine cycle, while the valve motion was continuously monitored using a proximity sensor.The gas sampling system was utilised on a direct injection diesel engine co-combusting a range of hydrogen-diesel fuel and methane-diesel fuel mixtures. In-cylinder gas sample composition was investigated at two sampling locations; within the diesel fuel spray and between adjacent spray cones. Concentrations of NOx were found to be higher between the two diesel sprays relative to within the spray cone for both hydrogen and methane addition. In the case of hydrogen-diesel fuel co-combustion, the particulate levels were observed to be higher in the diesel fuel spray relative to between two sprays; however, in the case of methane-diesel fuel co-combustion, higher particulate levels were measured in the region between the two sprays. This was attributed to methane contributing significant quantities of particulates to the total particulate concentration produced from the methane-diesel fuel mixture in between two sprays.