Merthiolate (Thiomersal) is known to be used as antimicrobial agent in inactivated vaccines without affecting vaccine potency. The present work investigated the effect of thiomersal contents in ND, AI and IBD inactivated vaccines on liver and kidney functions of vaccinated birds. The histopathological effect and the withdrawal time of such mercurial product from vaccinated chicken muscles were also investigated. Results revealed that residual thiomersal contents in ND, AI and IBD were 0.03; 0.02 and 0.03mg/ml respectively. Liver and kidney function parameters showed significant increases in serum activities of alanine aminotransferase (ALT) and serum aspartate aminotransferase (AST) up to the 4th week post vaccination. Serum urea was significantly decreased on the 3rd week in vaccinated birds compared to control ones. Significant increase in serum creatinine in vaccinated chickens was recorded on the 5th week post vaccination. Liver and kidney functions’ parameters remain high allover the experimental period (8 weeks). The histopathological examination of liver specimens revealed degeneration of hepatic cells and congestion of the central vein with inflammatory cell infiltration and congestion of blood vessels as well as coagulative necrosis. The spleen of vaccinated chickens showed depletion of lymphocytes while lungs showed thickening of the alveolar. Mercury contents in muscle were 0.72, 0.52; 0.046 and 0.00 mg/kg on the 1st, 2nd, 3rd and 4th week post last vaccination that considered safe to the consumer. It is recommended that vaccinated poultry with inactivated vaccines containing thiomersal should not be slaughtered before at least 4 weeks and it is preferable to use combined inactivated vaccines to reduce the thiomersal contents as possible.