Effects of acute prenatal hypoxia (13–14 days of gestation, 3 h, O2 = 7%) on acetylcholinesterase (AChE, EC 3.1.1.7) activity in homogenates, synaptosomes, and cytosol of the motor-sensory cortex of Wistar rats were studied on the days 1, 5, 10, 19 and 30 after birth. In homogenates of normally developing cortex, the AChE activity did not significantly change with age. Activity of AChE in synaptosomes increased 4 times throughout the entire period of observation, while in the cytosol, 4.3 times to reach maximum at the 19th day. Maximum rise of the AChE activity in synaptosomes was observed at the period from the 5th to the 10th day. Activity of AChE in homogenate and synaptosomes of rats submitted to prenatal hypoxia decreased during the first five days after birth (p < 0.001) but later, starting from the day 10, it increased in all fractions. A statistically significantly higher activity of AChE than in controls was revealed in homogenate of the motor-sensory cortex on day 19 (p < 0.01), while in synaptosomes, on the days 19 and 26 (p < 0.001 and p < 0.05, respectively), and in cytosol, on the days 10, 26, and 30 (p < 0.05, p < 0.05, and p < 0.001). Maximum change in the ratio of AChE activities in cytosol and synaptosomes was found on the day 19 (p < 0.01). At the same period of development, changes in the ratio of AChE activity in synaptosomes and homogenate of the control and hypoxic animals were also observed. Thus, prenatal hypoxia leads to in changes in the activity both of the cytosol and synaptosomal membrane-bound forms of AChE in the motor-sensory cortex of rats, which agrees with our own and literature data on disorder of neuro- and neuritogenesis in the process of formation of CNS and of behavioral reactions in early postnatal ontogenesis under the effect of pathogenic factors at certain days of prenatal ontogenesis.