BACKGROUND: Biocontainment protocols are critical for conducting infectious disease (ID) research, particularly when using small animal models in biosafety level (BSL) 2/3 environments. This study evaluates the impact of poly-methyl methacrylate (PMMA) containment vessels on the performance of preclinical positron emission tomography (PET) systems. We tested containment vessels designed with varying wall thicknesses (3, 6, and 9 mm) to simulate ID imaging facility equipment and protocols. Through the use of multicomponent phantoms and in vivo mouse models of Staphylococcus aureus infection, we assessed key performance metrics including count rate, image quality, activity recovery, and spatial resolution. RESULTS: The results indicate that the use of PMMA containment causes only minor reductions in imaging performance. The thickest PMMA (9 mm) led to a maximum 6.8% decrease in count rate, which remains well within the acceptable range of variation. Effects on spatial resolution were most noticeable for smaller structures within the phantom study, with a 19.65% difference in full width at half maximum (FWHM) for the thickest walled vessel. In vivo, using infected mice, the containment devices had modest effects on the task of activity concentration to be detected at the infection site, even with the thickest PMMA tube. CONCLUSION: These findings suggest that PMMA biocontainment vessels have small but measurable impact on preclinical PET system performance, making them a viable and cost-effective solution for conducting infectious disease imaging under BSL-2/3 conditions. Specifically, the thinnest containment (3 mm) had only minor effects on all tested parameters, suggesting it is well-suited for use in ID enclosures while maintaining accurate qualitative and quantitative assessments. This approach may reduce the burden for fully separate and specialized modifications for BSL-3 imaging facilities, and can be broadly applied to preclinical research involving pathogenic organisms.