Organic farming aims to be environmentally sound, but the question as to whether organic cropping brings more nutritional benefits to farmers and consumers than the conventional cropping needs still to be answered. To gain insights into the molecular effects of organic farming we used proteome analysis to analyze cabbage (Brassica oleracea L. var 'capitata') and carrot (Daucus carota var. 'sativus') Our aim was to identify the metabolic pathways that are affected by different cropping regimes and thus, may have an effect on quality, storability and pathogen resistance of crops. By means of two dimensional gel electrophoresis and MALDI tandem mass spectrometry we compared proteomes of cabbage and carrot root, obtained in the first growth season, cropped under three different schemes. These included a conventional scheme (C) and two organic schemes, O1, in which nutrients were delivered in a form of slurry, in accordance to regulations of organic farming and O2, in which nutrient supply was based mainly on autumn green manures. Proteins were extracted from lyophilized plant tissues into a buffer containing high concentrations of urea/thiourea, two detergents and reducing agent. This approach allowed short handling times of fresh plant materials. In the case of cabbage samples, the abundance levels of 58 out of more than 1300 quantified protein spots varied significantly between conventional farming and any of the organic cropping systems. Proteome profiles were also very similar between carrot root samples, where 68 out of 1800 resolved protein spots varied significantly. Proteins of the glycolytic pathway and Krebs cycle as well as several proteins related to amino acid and protein metabolism were overexpressed in organically farmed cabbage. Proteins related to detoxification processes were overexpressed in conventionally grown cabbage. Proteins involved in metabolism of carbohydrates, polypeptides and secondary metabolites were affected by different cropping regimes in carrots. The proteomes of conventionally grown vegetables varied from organically grown vegetables to a larger extent than the two organic cropping schemes varied from each other. In conclusion, this proteomics platform is suitable and useful for systematic studies of the effects of organic and conventional farming techniques on plant metabolism.