Abstract Naturally occurring nonecapsulated Streptococcus pneumoniae (NESp) are found worldwide and can cause invasive infections. In contrast, encapsulated pneumococci that fail to express capsule are rapidly cleared from the blood of infected mice. We previously demonstrated that NESp expressing the Ami-like proteins AliC and AliD are able to evade complement-mediated killing. Data indicated that factor H (FH) failed to bind to NESp, and thus did not reduce complement activation as seen in FH binding pneumococci. Proteomic data have shown that deletion of aliC and aliD altered pneumococcal protein expression. Additionally, NESp expressing AliC and AliD caused invasive pneumococcal disease in C1q-deficient mice. The purpose of this study was to examine the regulated pneumococcal genes in complement evasion by NESp. Flow cytometry was used to examine binding of C3b to NESp. A mouse model of infection was used to investigate complement interaction with NESp in vivo. NESp expressing AliC and AliD were able to persist for at least four days following intravenous infection of mice. Deletion of aliC and aliD resulted in the clearance of NESp within 24 hours post-infection. There was a four-fold increase in C3b deposition on the mutant NESp compared to the wildtype. Choline binding protein AC (CbpAC), a variant of pneumococcal protein A (PspA), was found to have reduced expression in the aliC and aliD deleted mutant. C-reactive protein (CRP) showed increased binding to NESp in which cbpAC was deleted. Regulated expression of CbpAC in NESp is able to overcome the innate immune response and lead to persistence of NESp within the host by reducing C1q deposition and arresting classical complement activation. Supported by Departmental research funds.