The human immune response to invasive microbes consists of two major arms: the innate and the adaptive response. The innate response occurs rapidly after infection, when the host tries to contain or inactivate the microbe. Two proteins involved in this process are C-reactive protein (CRP) and serum amyloid A (SAA), which are often elevated in the blood during an inflammatory response. In this study, the researchers analyzed CRP and SAA in the blood of people with varying stages of Lyme disease. They found that compared to healthy people, CRP was elevated in early Lyme disease, when patients had erythema migrans (EM) skin rashes. In contrast, CRP levels in patients with early or late neurological symptoms and arthritis were similar to healthy controls. However, patients with post-treatment Lyme disease syndrome (PTLDS) had higher CRP levels that those who recovered, suggesting ongoing inflammation in patients with long-term Lyme disease. SAA was elevated in patients with EM rashes, but was similar to healthy controls in all other patients, including those with PTLDS. These findings suggest that persisting symptoms after antibiotic therapy are associated with elevated CRP, and pave the way for further studies to understand long-term inflammatory processes in these patients.