This study was conducted to assess the Hazard Analysis and Critical Control Point (HACCP) system in a pasteurized juice production line through follow up prerequisite programs (PrP), Good Manufacturing Practices (GMP) and Critical Control Points (CCPs), the results were then compared to the standard specification. A total numbers of 361 samples were collected from the production line in local company including fruit concentrates, water, food contact surfaces, personnel swabs, environmental air and finished products samples. Standard methods were used to determine Total Plate Count (TPC), yeasts, moulds, coliform, heat resistant moulds and acid tolerant bacteria (Alicyclobacillus). Most of investigated samples were out of the standard acceptable ranges. The percentages of TPC, yeast and moulds in samples collected from fruit concentrates, food contact surfaces, water samples, personnel swabs, environmental air and finished products were significantly non-confirmed (22%, 85%, 41%, 44%, 14% and 4%), respectively. All these parameters counts lead to contamination in the products and cause high cost as a result of scraping these contaminated products. This was the first stage of problem evaluation and determining the CCP in order to overcome or reduce the phenomenon of microbial pollution in finished products.