This study evaluated the potential of opportunistic computed tomography (CT) for diagnosing underdiagnosed conditions such as sarcopenia, fatty liver, and ascites using a deep learning method. We analyzed 2,674 inpatient CT scans to identify discrepancies between imaging phenotypes derived from opportunistic CT scans and radiology reports and International Classification of Diseases (ICD) coding. We found that only 0.5%, 3.2%, and 30.7% of sarcopenia, fatty liver, and ascites diagnosed through opportunistic imaging or radiology reports, respectively, were recorded with ICD codes. This suggests that opportunistic CT can contribute to the advancement of precision medicine by improving diagnostic accuracy and the accuracy of risk-adjustment models.