Histamine intolerance (HIT) is a clinical condition caused by decreased intestinal degradation of ingested histamine, primarily due to reduced enzyme diamine oxidase (DAO) activity, leading to histamine accumulation and causing various clinical manifestations. The measurement of serum DAO is commonly used as the main diagnostic test for HIT, although its diagnostic use is still uncertain. In this retrospective study, we aimed to assess the validity of DAO determination in patients with clinically suspected HIT. We measured DAO levels in 249 patients with suspected HIT and 50 healthy adult controls without HIT-related problems. Based on five clinical criteria, we divided patients into two groups: high (all five inclusion criteria; 41 patients) and low probability of HIT (≤4 inclusion criteria; 208 patients). Patients with a “high probability of HIT” had the lowest DAO (median: 8 U/mL, IQR: 6–10) in comparison to patients with a “low probability of HIT (median: 10 U/mL, IQR: 7–16, p = 0.0006) and healthy controls (median: 18 U/mL, IQR: 14–22, p < 0.0001). The specificity and sensitivity for DAO levels < 3/< 10 U/mL (manufacturer’s set cut-off) to discriminate between patients with ‘‘high probability of HIT’’ and healthy controls were 100%/92% and 2%/71%. On the other hand, the specificity and sensitivity to discriminate between patients with ‘‘high probability of HIT’’ and ‘‘low probability of HIT’’ were 97%/61% and 2%/71%, respectively. Serum DAO determination represents an additional asset to the diagnosis of HIT based on clinical evaluation and assessment, but the diagnosis should not solely rely on DAO measurements.