End stage kidney disease (ESKD) patients are characterized to reduce bone strength due to disordering of calcium and phosphorous homeostasis. We demonstrate the use of Fourier transform infrared imaging and Raman spectroscopy to characterize bone quality in ESKD rats. Eleven-week male rats treated 5/6-nephrectomy and sham-operated rats were kept for 16 weeks, and then each femur was removed for measurements. We observe excess bone resorption compared to bone formation in ESKD rat, and bone mineral loss in endosteum is observed rather than in periosteum. We also find trabecular bone and epiphysis have a rapid turnover rate compared to cortical bone.