Biodiesel has become more attractive material for its properties such as biodegradability, renewability and very low toxicity of its combustion products. A higher quality of this fuel is essential in its potential commercialization. Analytical methods used in biodiesel analysis are constantly refined. The most popular analytical techniques include chromatography and molecular spectroscopy. The ATR-FTIR spectroscopy is one of the most important methods of spectroscopy. This paper presents the results of studies on selected oils of natural origin using ATR-FTIR infrared absorption spectroscopy. Three types of oils from pumpkin seeds and winter rapeseed were analysed. The main fatty acids were also determined in all the samples.