In recent years, there has been growing interest in estimating the degree of heating caused by the diagnostic ultrasound in clinical practice. Both theoretical and experimental methods have been suggested for estimating the heating potential, or thermal hazard, of diagnostic ultrasound. Aim of this study was to evaluate in vivo effects of ultrasound exposure of variable duration (from 10 up to 20 min) with commercially available imaging systems commonly used for diagnostic imaging. Numerical results related to the thermal effect are obtained by simulation program based on B-mode (scanning) and Doppler (non-scanning). To investigate the biological effects of the ultrasound exposure to the brain and liver tissues, the antioxidant enzyme activity and thiobarbituric acid reactive substances (TBARS) of the tissues were evaluated. In liver tissue, as a lipid peroxidation index, TBARS levels very significantly increase in Doppler group compared to control. However, in B-mode, TBARS levels are the same with the control group. Use of B-mode in foetal tissue is more reliable than Doppler mode because temperature rise is very small compared to the Doppler mode. On the other hand, the antioxidant enzyme activities tend to increase in B-mode and Doppler groups compared to the control group as a defensive mechanism. In the brain tissue, lipid peroxidation is increased slightly in B-mode compared to the control group. This situation is related to the molecular structure of the brain tissue because of its high lipid concentration. In brain tissue, the antioxidant enzyme activities and lipid peroxidation were significantly increased, such as liver tissue in Doppler groups. Doppler ultrasound may produce harmful effects in rat foetus liver and brain tissues as a result of the high temperature rises.