Abstract Background Human babesiosis is an emerging tick-borne disease in the US that is primarily caused by the protozoan Babesia microti (Bm). Although Babesiosis can cause life-threatening infections, the pathophysiology including host and parasite determinants associated with disease severity are largely unknown. The aim of this study is to identify parasite and host signatures of human babesiosis and correlate these with disease severity and long-term symptoms. Methods We enrolled prospectively patients with acute babesiosis (microcopy positive blood smear for Bm, confirmed by PCR) at Stony Brook University Hospital during 2020-2021. Blood samples and surveys were completed at initial diagnosis (Visit=1;V1) and at months 1, 6 and 12 (V2,V3,V4). Total RNA from whole peripheral blood was isolated using the PAXgene Blood RNA Kit from individuals infected with Bm and healthy controls. Quality of life (QOL) surveys were administered to patients. Results Peripheral blood transcriptome analysis of 17 patients (median age: 63 years, range 42-78; 24% female) who presented with babesiosis were distinctly different from uninfected individuals (n=9). Babesiosis was associated with a peripheral blood Type I and Type II Interferon transcriptional signature. Other dominant transcriptional signatures included those involved in activation of mononuclear cells, oxidative phosphorylation, inducible nitric oxide synthase and regulation of homeostasis as well as inducible nitric oxide synthase. Ingenuity Pathway Analysis for clinical chemistry and hematology also highlight changes associated with cardiotoxicity, hepatotoxicity, and nephrotoxicity as well as increased levels of red blood cells. Patients with babesiosis showed a persistent deterioration of QOL in cognition [mean V1=33.1; V3=36.3] and satisfaction [mean V1=28.4; V3=34]. Also a decrease in QOL over time despite effective treatment [mean at V1 82 (SD: 5.9), V2 80 (8.1), V3 76 (4.7) (p >0.05). Heat Map Summary. Volcano Plot Gene Pathways Analysis Conclusion Babesiosis is associated with a marked alteration in the peripheral blood transcriptome of patients that may also provide insight into both the pathophysiology of the disease including severity and complications. Furthermore, even after successful treatment, babesiosis may result in long-term impacts on quality of life indicators. Disclosures All Authors: No reported disclosures.