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I often hear different points of view to this question - some say the hottest part of the chili is its seeds, yet I've heard some (arguably more believable) sources claim that the white part that holds the seeds to the flesh is the hottest.

What part of the chili fruit is the hottest?

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oops... after editing chilli out in favor of chili I noticed OP is in Australia, where chilli appears to be the normal spelling. I don't appear to be enabled to rollback this edit, but it is still pending peer review so I hope that it either won't get 'approved' or can be rolled back quickly thereafter. –  Cos Callis Jul 4 '11 at 12:27
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2 Answers

up vote 18 down vote accepted

The Wikipedia article on Capsicum reads, citing a FAQ on a page of the ollege of Agriculture and Home Economics of the New Mexico State University:

Capsaicin is present in large quantities in the placental tissue (which holds the seeds), the internal membranes and, to a lesser extent, the other fleshy parts of the fruits of plants in the genus Capsicum. Contrary to popular belief, the seeds themselves do not produce any capsaicin, although the highest concentration of capsaicin can be found in the white pith around the seeds.

Cisneros-Pineda et al. measured via gas chromatography the content of capsaicin and dihydrocapsaicin in the pericarp, placenta, and seeds of seven cultivars of chili peppers and the results confirm this:

Capsaicon content

For dihydrocapsaicin, the difference is not so large, but the placenta still has a higher concentration.

In terms of concentration considering fresh mass the difference won't be as dramatic because while the seeds lose around half their mass by drying, the placenta will lose 90%.

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Both the seeds & the membrane can pack heat. While I believe the experts who say "it is the membrane" my experience is that it is easier to control the heat by removing the seeds and the membrane and adding some seeds back in to get to your target "heat level" in any giving recipe.

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removing seeds and spiciness? blasphemy! –  zanlok Jul 6 '11 at 1:10
    
"controlling" spiciness. Notice the part where I say "adding some back in." It helps to create consistency. –  Cos Callis Jul 6 '11 at 1:16
    
not at all, while I took it as tongue-in-check I thought it an opportunity to explain my reasoning... –  Cos Callis Jul 6 '11 at 1:37
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