Fruit juices are used for their nutritional value, thirst quenching properties and stimulating effect or for their medicinal values. Due to poor hygienic conditions during processing and packaging, fruit juices are becoming a health hazard. Many outbreaks are caused by consuming poor quality juices. Food borne infections are caused by eating food or drinking beverages contaminated with bacteria and parasites. Most of the food borne infections remains undiagnosed and unreported due to poor documentation system and failure in the implementation of law regarding food borne diseases in Pakistan. The present study was conducted to compare the quality of commercial fruit juices so as to provide data for local authorities to deal food security issue. A total of ninety packed fruit juice samples were obtained from retail shops in Lahore city. The fruit juice samples included, apple, mango and orange juices of five various brands. The pH value of the fruit juices measured using pH meter was found between 2.0 to 4.0. Bacterial load of fruit juices was assessed using Total viable count, Staphylococcal count and Coliform count to compare the quality of fruit juices.All the samples were positive for total viable count, 60 samples were positive for staphylococcus count and 30 samples ere positive for coliform count.The mean total viable count in fruit juice samples was3.70xIQ5CFU/ml (log 5.56±1.47CFU/ml)with the range from log 2.69 to log 7.67CFU/ml.Mean staphylococcal count in fruit juice samples was 1.34x 102CFU/ml (log 2.11±1.97CFU/ml) with the range from log 0.00 to log 5.62CFU/ml. Sixty out of 90 fruit juice samples showed staphylococcal counts.Mean coliform counts of 1.80xlOI CFU/ml (log 1.25±1.57CFU/ml) with the range from log 0.00 to log 5.50 CFU/ml. Thirty out of 90 fruit juice samples were positive for coliforms. Identification of bacteria was done on the basis of culture characters, microscopic characters and biochemical tests as per standard protocols described in Manual of Food Microbiology. Among the 226 bacterial isolates, Bacillus spp. were (150),Staphylococcusaureus (49)and E. coli (27), and no Salmonella were detected from the collected samples. Although fruit juices have low pH, still higher viable counts and prevalence of bacterial isolates suggest poor hygienic conditions during manufacturing procedures. Antimicrobial sensitivity profile of the isolates was studied by standard Disk diffusion method (Kirby Bauer method) for commonly used antibiotics. Among various antibiotics used, highest97.78% resistance toAzlocillinand lowest 25.22% resistance against Sulphafurazole. These findings suggest that the antibiotic resistance is transferred through fruit juices. After microbiological examination, it was cleared that fruit juices were as contaminated as compare to our country standards and hygienic conditions.