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While inspecting another problem I observed that most of the leaves are having two red dots (or very small bulbs, maybe cocoons) at the stems of their leaves: it is something harmful or even a pest? If so, do I need to do something?

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Possibly some kind of gall - pick one off and crack it open, see if there's tiny eggs or insects inside. – Bamboo Jul 7 '12 at 12:49
what kind of cherry tree? – kevinsky Jul 7 '12 at 23:24
up vote 7 down vote accepted

I turn the floor over to Mr. Chas. Darwin:

“Certain plants excrete sweet juice, apparently for the sake of eliminating something injurious from the sap; this is effected, for instance, by glands at the base of the stipules in some Leguminosæ, and at the backs of the leaves of the common laurel. This juice, though small in quantity, is greedily sought by insects; but their visits do not in any way benefit the plant.”

Cherries, too. If you look closely, there will be a pair of staggered glands on the leaf stems; sometimes prominently, like in the species you are growing (Prunus avium aka sweet cherry?), and sometimes far less so, as in the common wild black cherry of North America.

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although, these are possibly galls, too, but the location at the top of the leaf stem suggest that they are glands. If every leaf on your tree has them there, and nowhere else, then they are glands. – Steve K Jul 8 '12 at 13:56
They don't look like stipules though, particularly the one on the edge of the leaf. – Bamboo Jul 8 '12 at 17:54
The glands aren't stipules (and they are at the top of the petiole, not at the base), just knobby protrusions. – Steve K Jul 8 '12 at 18:56
@SteveK they are glands. They have now dried out - all of them. I have a sweet cherry and a cherry which is not carrying fruits (only big pink flowers) - both tree had those dots. – Patrick B. Jul 10 '12 at 10:16

They are extrafloral nectaries, or nectar glands. If you watch, you will probably notice beneficial insects and/or ants visiting them for the nectar they provide. You can just leave them be - they are supposed to be there.

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Aha, could this be why I get a steady stream of ants on my peach tree? The ants don't seem to cause any damage. – bstpierre Jul 16 '12 at 19:42

I found the answer here about 3/4 of the way down this page today on 6/21/15:

It is a defense mechanism of the tree to protect itself from caterpillars. The sweet sap of those nodes attract ants, which defend the food source (the sap) by attacking caterpillars.

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