An external cavity laser (ECL)-based off-axis cavity-enhanced absorption spectroscopy was applied to noninvasive clinical diagnosis using expired breath ammonia analysis: (1) the correlation between breath ammonia levels and blood parameters related to chronic kidney disease (CKD) was investigated and (2) the relationship between breath ammonia levels and blood concentrations of valproic acid (VAP) was studied. The concentrations of breath ammonia in 15 healthy volunteers, 10 epilepsy patients (before and after taking VAP), and 27 patients with different stages of CKD were examined. The range of breath ammonia levels was 120 to 530 ppb for healthy subjects and 710 to 10,400 ppb for patients with CKD. There was a statistically significant positive correlation between breath ammonia concentrations and urea, blood urea nitrogen, creatinine, or estimated glomerular filtration rate in 27 patients. It was demonstrated that taking VAP gave rise to increasing breath ammonia levels. A statistically significant difference was found between the levels of exhaled ammonia (NH3) in healthy subjects and in patients with epilepsy before and after taking VAP. The results suggest that our breath ammonia measurement system has great potential as an easy, noninvasive, real-time, and continuous monitor of the clinical parameters related to epilepsy and CKD.