The freezing of tomato could be a good method for tomato processing as well as using it as fresh fruit in time when tomato lacks on the market. In the present literature there is no information about freezing process of organic tomato. The aim of the work was to measure the influence of the farm management, kind of package and tomato cultivar on bioactive compounds content in frozen tomato fruits. For experiment three standard tomatoes (Mercury, Akord and Rumba) and two cherry tomatoes (Conchita and Picolino) were used. The fruits were obtained from two organic (certificated) and two neighboring production farms. After harvest tomato fruits were selected, washed and frozen. Two different kinds of package were used: plastic bags and vacuum bags. After six month of freezing tomato fruits were freeze-dried and chemical analysis was made. The content of dry matter (before freeze-drying), total and reducing sugars, acidity, vitamin C, carotenoids and polyphenols were measured. The obtained results showed that organic tomato contained significantly more dry matter, organic acids, vitamin C, gallic, chlorogenic acids, total flavonoids, myrycetin, kaempferol, and apigenin compared to conventional frozen tomato. The conventional frozen tomato contained significantly more total and reducing sugars as well as quercetin compared to organic ones. The vacuum packed tomato contained significantly more organic acids, vitamin C and quercetin compared to tomato packed in plastic bags. The fruits packed in normal, plastic bags (not-vacuum) contained significantly more dry matter, total and reducing sugars, lycopene, phenolic acids and flavonoids (without quercetin). Among the examined cultivars cherry fruit Conchita cv. had the best nutritive value after freezing and among standard tomato - Rumba cv