Self-ignition engines are currently used to drive lorries, agricultural and road construction machines, as well as passenger cars. Common Rail supply systems are widely used in such engines. Arguments for using these systems include the simple construction of a system as well as practically unlimited control of fuel feeding (division of a fuel dose into several portions), which allows for controlling the fuel combustion process. This facilitates optimisation of the combustion process in limiting toxic emissions, which is the main evaluation criterion for modern combustion engines. Operation of an engine with a Common Rail system is controlled by an Electronic Diesel Control (EDC), which is responsible not only for controlling the supply system, but also for the diagnostics of the whole engine. The diagnostic monitors embedded in the controller supervise the operation of the supply system, but also of the whole engine, including the systems responsible for reducing toxic emissions released to the atmosphere, in accordance with the European On Board Diagnostic (EOBD) standard. Unfortunately, despite sophisticated diagnostic functions, defects sometimes occur in vehicles with engines with a CR system, which are not signalled by EOBD systems. In such cases, an additional tool is needed to help a diagnostician to identify the cause of improper operation of an engine. This article presents several examples to describe the diagnostics of a Common Rail system using an analyser of diagnostic electric signals to detect the cause of such defects.