The internal ribosome entry site (IRES) from the picornavirus family has frequently been used to express multiple genes from a polycistronic message in retroviral vectors. While examining factors affecting levels of gene expression in IRES-containing retroviral vectors, it was found that retroviral vectors expressing the two genes linked by IRES, the reporter gene and the selectable marker neo, produced significantly lower levels of protein than those containing a reporter gene alone. This observation has been made with various cDNA sequences. However, when the neo was replaced with a different cDNA, the level of gene expression was increased, often to the level achieved with a vector expressing a single gene, suggesting that the bacterial neo sequence has a negative effect on expression. Analysis of the steady-state RNA levels isolated from transfected packaging cells showed that the neo-containing retroviral vectors produced significantly lower levels of RNA than those lacking this bacterial sequence indicating that neo interferes with expression of the neighboring gene at the level of RNA. Furthermore, the order of genes in the IRES-neo-containing vectors appeared to be more important than in the vector lacking the neo sequence. Our results suggest that neo has to be used in the retroviral vector with care, especially when a high level gene expression is needed.