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Chocolate causes me to have a bad headache within 10-15 minutes, sore throat and "down" feeling for several days. Why? I know it has theobromine. Does it have an effect on seritonin?

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I also react in a similar way to chocolate (and other foods)
chocolate (pods?) are fermented this increases amine levels (and flavour) dark chocolate is higher in naturally occuring chemicals. all chocolate contains Phenylethylamine, a vaso dilator that acts as a headache trigger for sensative people.
you may want to check out diets for migraine sufferers and you will find related info on other amne rich foods
here is a quote from one allergy site:

"Vaso-active amines in food – natural histamine.

Histamine like substances occur naturally in foods and can trigger symptoms that mimic allergy. This is particularly true of fermented foods that contain high quantities of the vaso-active amines such as Histamine, Phenylethylamine, Serotonin, Tyramine and Dopamine.

Histamine is contained in a number of foods. It occurs in 3 cheeses (Blue, Roquefort and Parmesan), 2 vegetables (Spinach and Aubergine), 2 red wines (Chianti and Burgundy) and yeast extract or Marmite. Tyramine is found in Camembert and cheddar cheese, pickled herring, fermented sauces like bean and Soya, and in chicken livers. Serotonin is in banana, kiwi fruit, pineapple, tomato, walnuts, figs, plum and even seafood such as octopus. Symptoms of vaso-active amine ingestion are cramping, flushing, headache, palpitations and hypotension. The symptoms are usually dose related and occur when the histamine metabolising enzyme diamine oxidase is saturated and cannot metabolise the histamine ingested. Symptoms are most unpleasant but not usually life-threatening."

allergy-clinic.co.uk/food_allergy_for_doctors.htm
hope that helps
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