Q. Do the very common brown spots on the yolk of organic eggs make them not kosher?

A. Organic eggs have restrictions in the way their mother-chickens are grown and fed. Egg-laying chickens cannot be raised with antibiotics or growth hormones and must be given organic feed that is produced without using conventional pesticides or synthetic fertilizers. Organic eggs have statistically more blood spots and brown spots than common eggs
However Darkei Teshuva (Y.D. 66: 23) permits brown spots in eggs.
OU site (Eggs and Blood spots – June 20, 2006) defines these spots as “protein spots.” They are by far the most common blemishes found. They are formed by a microscopic “seed” of foreign matter that enters the egg during the early stages of development. Though found in both brown and white eggs, they are more prevalent in brown. Generally, these look like thick clear jelly in the egg-white and may be any size. If the “seed” speck is visible, it looks like a reddish brown piece of dirt at the center of the spot. Whether in the white or yolk, these blemishes present no Halachic concerns and the eggs may be consumed without further action.” A similar pinion is to be found on the CRC siteHorav Shlomo Miller’s Shlit’a opinion is also to be lenient on brown spots.

Rabbi A. Bartfeld as revised by Horav Shlomo Miller Shlit”a