Spinal cord injury and cyclophosphamide-induced cystitis dramatically alter lower urinary tract function and produce neurochemical, electrophysiological, and anatomical changes that may contribute to reorganization of the micturition reflex. Mechanisms underlying this neural plasticity may involve alterations in neurotrophic factors in the urinary bladder. These studies have determined neurotrophic factors in the urinary bladder that may contribute to reorganization of the micturition reflex following cystitis or spinal cord injury. A ribonuclease protection assay was used to measure changes in urinary bladder neurotrophic factor mRNA (βNGF, BDNF, GDNF, CNTF, NT-3, and NT-4) following spinal cord injury (acute/chronic) or cyclophosphamide-induced cystitis (acute/chronic). The correlation between urinary bladder nerve growth factor mRNA and nerve growth factor protein expression was also determined. Each experimental paradigm resulted in significant (P ≤ 0.05–0.005) changes in urinary bladder neurotrophic factor mRNA, although the magnitude of the changes differed between paradigms. Urinary bladders from rats with acute spinal cord injury (4 days) exhibited the largest increase in neurotrophic factor mRNA levels (βNGF, 21-fold increase; BDNF, 78-fold increase; GDNF, 11-fold increase; CNTF, 5.5-fold increase; NT-3, 10-fold increase; NT-4, 25-fold increase) relative to control urinary bladders. More modest but significant increases were demonstrated for urinary bladders from rats with chronic (4–6 weeks) spinal cord injury. Significant increases in urinary bladder neurotrophic factor mRNA levels of comparable magnitude were demonstrated following either acute or chronic cyclophosphamide-induced cystitis. Increased abundance of urinary bladder nerve growth factor mRNA was not always associated with increased total urinary bladder nerve growth factor. Total urinary bladder nerve growth factor decreased following acute or chronic cystitis despite increased abundance of nerve growth factor mRNA. Urinary bladder nerve growth factor mRNA correlates with protein measures 5–6 weeks following spinal cord injury but not earlier. The 5- to 6-week time point coincided with the reemergence of the spinal bladder-to-bladder reflex mechanisms following spinal cord injury. Discrepancies between two measures (mRNA and protein) may reflect retrograde axonal transport of nerve growth factor to the dorsal root ganglia (L6–S1). Retrogradely transported NGF may play a role in altered lower urinary tract function following spinal cord injury or cyclophosphamide-induced cystitis.