Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) are organic surfactants widely used in various industrial and consumer applications. Due to their chemical properties, these perfluorinated compounds (PFCs) have also become persistent contaminants. The risk of possible intrauterine and lactational exposure to these chemicals poses a significant health concern for potential developmental effects. In the present study we have found that dietary exposure of mice to 0.3 mg/kg of PFOS or PFOA throughout pregnancy results in different distribution pattern in the offspring brain and liver. In particular, exposure to PFOS led to four times higher accumulation of the chemical in the brains of newborn mice than PFOA. We have used a battery of behavioral tests to evaluate motor function, circadian activity, and emotion-related behavior in the exposed offspring. Exposure to PFOS resulted in decreased locomotion in a novel environment and reduced muscle strength only in male offspring. Prenatal exposure to PFOA was associated with changes in exploratory behavior in male and female offspring, as well as with increased global activity in males in their home cage. The neurobehavioral outcome of prenatal exposure to PFCs in mice is characterized by mild alterations in motor function and it appears to be sex-related.