Borrelia burgdorferi, the causative agent of Lyme disease, lacks the ability to biosynthesize many essential nutrients de novo, including N-acetylglucosamine (GlcNAc). This amino sugar is required for cell wall synthesis, and is a component of the complex growth medium used for in vitro propagation. When cultured without free GlcNAc, B. burgdorferi cells exhibit a unique biphasic growth pattern. We hypothesized that genes involved in the GlcNAc starvation response would be differentially expressed when compared to cells cultured in complete medium, and investigated this using transcriptomics. Twenty-one genes were differentially regulated in wild-type and starvation-adapted cells cultured without GlcNAc compared to wild-type cells cultured with GlcNAc. Of those, three genes involved in carbohydrate utilization were upregulated: bbb04 (chbC) encoding a subunit of the chitobiose transporter, bb0629 (fruA-2) encoding a putative carbohydrate transporter and bb0644 (nanE) encoding a putative GlcNAc-6-phosphate-2-epimerase predicted to catalyze the conversion of N-acetylmannosamine-6-phosphate (ManNAc-6-P) to GlcNAc-6-P. Quantitative RT-PCR was used to confirm differential expression of select genes, and substitution of free GlcNAc with free ManNAc resulted in growth to high cell density, suggesting B. burgdorferi cells can utilize free ManNAc for cell wall synthesis and energy production.