Whereas there are many different causes of histamine intolerance, poor gut health is the number one cause! Histamine intolerance originates in the gut! Does it seem like every time you have a glass of wine, cheese, you get a headache or even a migraine? You might have histamine intolerance. Both cheese and wine are high in histamine, a chemical produced during the fermentation process of making wine and cheese. Poor gut health leads to poor degradation of histamine.