Mercury is one of the heavy metals that enter the environment through natural and anthropogenic processes. Birds have been used as biological indicators for mercury contaminations in the environment due to their direct contact to aquatic environments for water and food and birds are particularly useful as bioindicatorsof pollution because they are often high in the food chain. In birds, organs including liver and kidney are best to show the presence of mercury and these organs accumulate the mercury through time. Feathers have been also used to show the mercury contaminations. In this study, bio-accumulation of mercury in birds in three organs including liver, kidney and hyperpnoea at three sites in Isfahan was investigated. Forty samples of birds from Landfyl, Shahin Shahr wastewater treatment area and Zayandehrood River were collected in winter 1389 and spring 1390. These regions supports diverse ecosystems and biota in need of remediation and protection, and metal data from these regions is needed. Biometric measurements were conducted on the samples, samples dried in the oven and then the amount of mercury was measured after digestion twice by atomic absorption spectroscopy. The software (Version 16) was utilized to analyze data. Mercury levels in the liver, kidney and hyperpnoea were 8 to 68880 , 0 to 7817 and 0 to 8978 respectively. Amount of mercury in these three organs without significant differences was hyperpnoea liver kidney. According to the results, in these three organs, Zayanderod samples showed more contaminations than other sites. The lowest mercury levels were recorded in vegetarian birds. The average mercury value in liver was 1543 , which is less than the amount of mercury (125-49 ppm) which can cause death in birds. The average value in kidney was 1284 and less than the amount of mercury (5-13 ppm) which can cause nephron toxicity. However four samples of aquatic and animal consumers showed more mercury than the above. The average value obtained for hyperpnea was 2002/2 , less than the amount of mercury (5 ppm) which reported harmful for health and reproduction of birds. However, in five samples of Zayandehrood, mercury was recorded more than this value. The average amount of mercury in the three organs was correlated to body weight. It seems that although these values in all organs were less than legal values, these mercury values in Zayandehrood River are alarming. More research in this area is recommended to understand the mercury resources and its accumulation processes in the environment. The average mercury value in breast feather was 2061/25 that mercury level was 296 to 5934 . Keywords : bio- accumulation, mercury, birds, liver, kidney, hyperpnea, Isfahan