In the period 2011–2015 we conducted three experiments in the Gorenjska region in which we analysed morphological parameters of the taproots and the content of metabolites in carrots (Daucus carota L.) grown according to the organic and integrated growth guidelines. The content of primary and secondary metabolites was analysed with high performance liquid chromatography and mass spectrometry (HPLS-MS). We considered cultivar ('Rodelika', 'Fanal' and 'Rolanka'), type of fertiliser (organic and mineral), the increased amount of nitrogen and potassium and the year of growth. In both growing systems the added nutrients significantly increased the yield of all cultivars (from 47 % to 262 %) as compared to the control plots (not fertilised). Organically grown carrots contained significantly less malic acid (43 %), fumaric acid (19 %), and shikimic acid (23 %). On the other hand, they contained more pyruvic acid (80 %) and ascorbic acid (12 %) compared to the carrots from the integrated growth system. The content of phenolic acids and carotenoids dependend on the cultivar. 'Fanal' contained 30 % less carotenoids than 'Rodelika' and 'Rolanka'. 'Rolanka' taproots contained 21 % and 48 % more phenolic acids than 'Rodelika' and 'Fanal' respectively. The increased amount of added nitrogen and potassium influenced saccharose content which was increased by 10 %, and reduced the amount of ferulic acid derivatives by 105 % as compared to the less heavily fertilised carrots. The taproots of unfertilised carrots contained less saccharose (37 %), less malic acid (64 %), more ascorbic acid (10 %) and more ferulic acids derivatives (74 %) with regard to the increased fertilisation with nitrogen and potassium. Taproot maturity significantly influenced all the metabolites we had analysed while the year of growth only influenced glucose content (65 % less), malic acid (36 % more), ascorbic acid (26 % less) and phenolic acids (160% more in 2012 as compared to 2011). In the third experiment, which was a pot experiment, we grew carrots for the analysis of the isotopic composition of nitrogen which would serve as a marker in determining growing system (organic or integrated). Using organic or mineral fertiliser, respectively, significantly influenced the isotopic composition of nitrogen in the carrots (organically grown carrots contained from 47 % to 107 % more of the heavier isotope 15N than the ones fertilised with mineral fertilisers, however, the method of isotopic composition δ15N is not accurate enough to be used as a sole criterion in determining the authenticity of organic growth.