Question: What’s the diagnosis code for CPAP intolerance? Answer: Continuous positive airway pressure (CPAP) intolerance means that the CPAP treatment is ineffective in treating the patient. Since the patient is being administered the CPAP treatment for a sleep apnea diagnosis, you should list this as the primary diagnosis, if available. You may report CPAP intolerance as a secondary diagnosis using code Z78.9 (Other specified health status).