Agassiz's desert tortoises (Gopherus agassizii) are subjected to a myriad of ecological and environmental stressors as human development and land use practices increase across the Mojave Desert, USA. Despite more than 20 years of intensive efforts to improve conservation for this threatened species and desert ecosystems, tortoise populations continue to decline. To improve the assessment of health and immune function, I investigated how tortoises respond to a variety of environmental and ecological conditions using gene-based diagnostics. Gene transcription profiling measures an individual's change in physiological status by quantifying the amount of messenger RNA (mRNA) that is transcribed for targeted genes in response to intrinsic and extrinsic stressors. I incorporated transcript profiling into a series of experiments with both captive and wild tortoises to measure their responses to various drivers. I found that native plant diets frequently intermixed or replaced by the non-native grass Bromus rubens negatively influence the physiological ecology, immune-competence, health, and survival of young tortoises, highlighting the negative indirect effects of invasive plants in desert ecosystems (Chapter 1). Additionally, I improved the assessment of animal health by combining standard analytical blood diagnostics (e.g. hematological, biochemical, trace elements) with transcript profiles in both clinically abnormal and normal tortoises (Chapter 2). Necropsy and histology evaluations from clinically abnormal tortoises revealed multiple physiological complications. Transcript profiling proved to be important for the identification of ill tortoises, as they increased molecular reactions for genes responding to environmental toxicants, oxidative stress, microbial and bacterial infections, and malnutrition. Lastly, I monitored health responses following a facilitated transmission of the pathogenic bacteria, Mycoplasma agassizii, in naïve adult individuals and measured innate and induced immune reactions in tortoises over time (Chapter 3). This work revealed that infected tortoises were able to transfer M. agassizii to naïve tortoises within 30-60 d; however, it took ~1.5 yr for these individuals to elicit an induced antibody response specific to M. agassizii. I found no differences in transcript profiles in tortoises (control, exposed, infected, reference) before or during the first three months of the experiment; however, exposed and diseased tortoises down-regulated their over-all immune responses the following spring (222 d post exposure) as they emerged from winter dormancy. Collectively, transcription profiling proved useful in tortoises to help identify animals responding to various intrinsic and extrinsic stressors, and aided in providing insights needed to understand immune function in vertebrate ectotherms.