Streptococcus pneumoniae is known as an opportunistic pathogen which belongs to the most common etiological agents of local and systemic diseases in humans. In immune compromised patients, pneumococci infiltrate the meninges and cause life threatening inflammation. Recently, we have established a transwell-based Blood Brain Barrier (BBB) model with human endothelial-like cells and astrocytes providing a reliable tool to study pathogenesis mechanisms of bacterial and parasitical transmigration of the cellular barrier between vascular system and cerebral tissue. We applied this model with the aim to study the role of the polysaccharide capsule of a clinical isolate from a meningitis patient identified as a highly virulent serotype 7F pneumococcus. After optimization of the transformation procedure for this clinical isolate, we successfully deleted the capsule gene locus and confirmed loss of capsule expression by southern blot hybridization and electron microscopic visualization. In consistence with the already described inhibiting effect of capsular polysaccharides on phagocytosis by macrophages, the serotype 7F strain was more efficiently endocytosed by human monocytes (U937) as the corresponding capsule deficient mutant. Infection analyses using the BBB model with the serotype 7F wild type isolate and the mutant strain demonstrated a significantly reduced transmigration activity of the capsule-deficient serotype 7F. These results were further confirmed by infection of a second blood brain barrier model using Human Brain Microvascular Endothelial Cells (HBMEC). Interestingly, a collection of serotype 7F strains isolated from cerebral liquor or blood of children suffering from meningitis revealed a higher transmigration capacity as monitored in comparable infection studies with serotype 7F isolate derived from a non-invasive colonization. These data shed new light on the role of pneumococcal capsule in invasive infection process of the cerebral tissues and underline the requirement of adequate infection models to elucidate the diversity of highly virulent clinical isolates.