The aim of this study is to investigate the combustion process and pollutant formation in a small compression ignition engine. The engine is a prototype for quadricycles. It was designed to comply with Euro 4 emission standard that is a future regulation for this type of vehicles. Two optical accesses for endoscopes were realized in the first cylinder to investigate the combustion process. Two-color pyrometry method was applied to combustion images in order to detect the flame temperature and the soot concentration. The engine ran with a biodiesel, the rapeseed methyl ester, and a conventional diesel fuel. Operating conditions at the engine speed of 2000 rpm at full and medium load were tested. NOx emissions were measured at exhaust. A smoke meter was used to determine the particulate matter concentration. The sizing and the counting of the particles were performed by means of an engine exhaust particle sizer spectrometer. A correlation between in-cylinder data of flame temperature and soot concentration with NOx and PM emissions, respectively, was found. Emission reduction when the engine ran with RME was observed.