Therapy for central nervous system (CNS) diseases requires drugs that can cross the blood-brain barrier (BBB). BBB disruption has been reported in patients with multiple sclerosis (MS) and Alzheimer's disease (AD) and the related animal models as evidenced by increased infiltration of inflammatory cells or increased staining of Igs in the central nervous system. Although CNS penetration of therapeutic agents under pathological conditions has rarely been investigated, it is commonly assumed that BBB disruption may lead to enhanced CNS penetration and also provide a "window of opportunity" through which drugs that do not normally cross BBB are able to do so. In this article, we have compared brain penetration of eight small molecules in naive animals and experimental autoimmune encephalomyelitis (EAE) mice, streptozotocin-induced mice, and TASTPM transgenic mice. The tool compounds are lipophilic transcellular drugs [GlaxoSmithKline (GSK)-A, GSK-B, GSK-C, and naproxen], lipophilic P-glycoprotein (P-gp) substrates (amprenavir and loperamide), and hydrophilic paracellular compounds (sodium fluorescein and atenolol). Our data showed that rate and extent of CNS penetration for lipophilic transcellular drugs and P-gp substrates are similar in naive and all tested animal models. The brain penetration for paracellular drugs in EAE mice is transiently increased but similar to that in naive mice at steady state. Our data suggest that, despite reported BBB disruption, CNS penetration for small molecule therapeutic agents does not increase in MS- and AD-related animal models.