The quality indicators of fuels for combustion engines are in the Czech Republic being monitored by The Customs Administration of the Czech Republic and The Czech Trade Inspection Authority. Moreover, in filling stations like 'Benzina', these indicators are secured by the monitoring called 'The Seal of Quality', which is performed by the technicians from the SGS Czech Republic laboratories. The aim of the aforementioned precautions is not only to secure the quality indicators of the fuels, but also to prevent the environmental hazards and secure the economic and tax policy of the state. Despite this monitoring, the results from the preventive inspections are still showing a rather alarming number of filling stations that are showing operational and seasonal divergences in terms of fuel quality indicators. These unwanted divergences are mostly caused by the transport from the producer to the filling stations. For example, after switching between various types of fuels that are transported by a particular cistern or any other type of tank, the fuels might get contaminated from each other. The contamination might be caused on purpose, by 'enhancing' the fuel with other substances. For example, those with a different rate of taxation than a particular fuel. Such procedure leads to degraded quality indicators and there is a side effect of tax evasion, too. Currently, the monitoring of the fuels is conducted in a special laboratory. Therefore, the need for a suitable operational identification method arose. This paper presents the summary of the author´s knowledge and expertise, gained in the area of identification and diagnosis of fuel quality indicators in combustion engines. Fuels for diesel engines have been evaluated. The original hypothesis of the author that the infrared spectra can be utilized not just for identification of the fuel but also for evaluation of the fuel quality indicators was successfully confirmed by the outcomes. Changes in fuel parameters are reflected in a variation of absorbance values and spectrum widths. The creation of infrared spectrum databases leads to a routine diagnosis of fuel in operational practise.