During the last decade, the increasing demand of food safety has stimulated research regarding the risk associated with consumption of foodstuffs contaminated by contaminates especially heavy metals. Tomatoes and their products provide an essential source of vitamin C, potassium, and antioxidants. Iran is the 7th biggest producer after Egypt and Italy with 4,826,396 tons according to the data of “Food and Agriculture Organization of The United Nations”. Regarding to the high consumption of tomato paste in this study, the levels of lead, cadmium, copper, zinc, tin and iron in fresh tomato and in tomato canned paste as well as the histamine content of tomato paste are reported. Due to this descriptive study the effect of processing method; samples were studied in 2 different conditions: fresh and canned paste forms. Fresh Tomato samples were collected during the spring 2014 from five regions of Fars and Kermanshah province farmlands. A total of 480 symptomatic samples were collected from 24 fields located in Fars and Kermanshah Provinces. Meanwhile 400 canned tomato pastes from 12 popular brands in 3 consequences months were purchased. All canned paste samples had the same date of producing. Samples were randomly purchased for analysis and analyzed according to standardized international protocols by wet digestion method. Histamine content was Determined by Capillary Electrophoresis while Lead, Cadmium , Zinc, Copper, Tin and Iron contents in fresh and canned paste tomato samples were determined by Atomic absorption spectrometer. According to variance analyses of data, Tin and most of the heavy metals in canned samples were significantly affected by storage time. The results showed that, the highest concentration in canned food samples was for tin, 357.88±14.33 and lowest 26.54± 5.73 ( mg/kg DW). According to variance analyses of data, heavy metal concentration and histamine in canned food samples were significantly affected by company factory. There was a positive correlation between the storage time and heavy metal contents especially tin, zinc and iron and they were varied significantly (p < 0.003 ) and after 6 and 12 months of storage the heavy metal contents were much higher in the same brand in comparison by the newer samples.