Following strict standards imposed on raw materials for food production, the most important aim in plant cultivation is to obtain high quality yields with desirable chemical composition. It can be achieved, for example, through fertilization, which modifies the content and share of organic components (protein, fat) in crops. This study was conducted in 2009, 2010, 2011, and dealt with the effect of nitrogen, sulphur and boron fertilization on the content and chemical composition of fatty acids in light- and dark-coloured seeds of oil flax. The content of saturated acids, with the following number of carbon atoms C8, C10, C12, C16,C18, C22, and unsaturated acids with carbon atoms C16:1, C18:2 and C18:3, was especially modified by the weather conditions. In 2009, with the lowest mean values of precipitation and air temperatures during the plant growing season, the highest content of oleic acid (19.94%) and MUFA (20.1%) was determined. In turn, the highest air temperature and mean precipitation values in 2011 favoured a high content of linolenic acid (64.3%) and PUFA (78.5%) Regardless of the year of flax cultivation, the dark-seed cultivar had a higher share of oleic acid C18:1, n-9 in the sum of fatty acids (by about 6%), and a lower share of linolenic acid C18:3, n-3 (by about 10%). The cultivar with light-coloured seeds accumulated higher amounts of capric, palmitoleic, behenic acids, as well as 6.7% more of palmitic acid and 5.3% more of linolenic acid than the dark-seeded cultivar. The three-year experiment demonstrated that the introduction of a nitrogen dose of 40 kg ha-1 was advantageous only to the accumulation of palmitic and stearic acids, while the simultaneous application of 15 kg B and 70 kg S ha-1 resulted in a decreased lignoceric acid content. The tested fertilization did not affect significantly the content of MUFA, PUFA and saturated fatty acids (SFA). No statistically significant differences were determined in the total content of saturated fatty acids in flax oil of the examined cultivars. The dark-seeded cultivar presented a higher value of mono-unsaturated fatty acids, by 19.3%, while the light-seeded cultivar Oliwin contained 4.4% more of essential unsaturated fatty acids. The average content of saturated fatty acids (SFA) in flax oil reached the level of 8.24%. The percentage of Essential Fatty Acids (EFA = PUFA – polyunsaturated Fatty Acids) was about 74.9%, while the percentage of MUFA (Monounsaturated Fatty Acids) was nearly 17%. In the experiment, the C18:2 (n-6) to C18:3 (n-3) ratio for the light-seeded cultivar was 0.24:1, compared to 0.32:1 for the dark -seeds variety. The ratio of saturated to unsaturated fatty acids reached 1:8.97 for the examined cultivars, being higher in the light-seeded cultivar.