Abstract Brucellosis is a zoonotic disease caused by Brucella bacteria, acquired by humans through contact with or consumption of products from infected animals. Treatment outcomes vary widely; some patients recover, others relapse, and others develop chronic symptoms despite therapy. We employed expression profiling using RNA sequencing (RNAseq) to better understand variation in outcomes and investigate disease mechanisms. We performed RNAseq analysis of whole blood samples from 125 Brucellosis patients and 51 healthy controls from Macedonia. Patients were subdivided based on disease history into primary, secondary, and chronic infection. Secondary and chronic cases did not show differences in gene expression from healthy controls or from each other. Primary cases displayed numerous transcriptional changes relative to healthy controls. Up-regulated genes were enriched for response to interferon-gamma, cytolysis, T cell proliferation, and cell cycle; down-regulated genes, for B cell proliferation. Primary cases were further subdivided based on outcome into those who resolved with treatment and those who developed disease relapse during treatment. In comparison to healthy controls, relapse cases showed larger magnitude differences in expression at diagnosis than resolution cases; this suggests that relapse could potentially be predicted based on transcription levels at time of diagnosis. Differences in gene expression observed at diagnosis were no longer present 6–9 months after diagnosis. Our results indicate opportunities to prognostically identify patients that may require more intensive treatment and monitoring, and to better understand the symptomology of and immune response to Brucella infection.