The worldwide consumption of blueberries has increased due to their potential health effects. They contain micronutrients, various phytochemicals and anti-oxidant pigments, represented especially by anthocyanins. In addition to these, carotenoids and fatty acids are also present. The aim of this study was the identification and quantification of carotenoids (by HPLC) and fatty acids (by GC with flame ionisation detection) in two bilberry genotypes (Wild 1 and 2) and three cultivars (BlueCrop, Elliot, and Duke). The main carotenoids identified were lutein, β-cryptoxanthin, and β-carotene, with the average total carotenoid content of 266 μg per 100 g of fruit. The ratio of saturated fatty acids (SFAs) to polyunsaturated fatty acids (PUFAs) was 0.098 for Wild 1 and 0.11 for Wild 2 genotypes and ranged from 0.14 to 0.28 for cultivars. The main fatty acids identified were linoleic (18:2) and linolenic (18:3) acids in all the samples analysed. In Vaccinium myrtillus the amount of carotenoids and fatty acids was higher than in Vaccinium corymbosum species.