Wheat germ is a byproduct of refined grains that have been stripped of their bran and germ. The germ left over from the manufacturing process is collected and sold separately, sometimes toasted and flavored and sometimes raw. It has a grainy texture and nutty flavor and is an excellent source of nutrients, including fiber, folate and essential fatty acids.
Bran
As the other missing part of the whole grain, isolated wheat bran is one of the best substitutes for wheat germ. People commonly use it for the same purposes, such as boosting the content of fiber in baked goods or cereals, and it has a similar texture and nutritional value. However, bran can be harder to find in stores and may be more expensive than wheat germ. If you can't seem to locate any wheat bran to use as a germ substitute, try using bran from other whole grains, such as rice, corn, oats, millet or barley. Baking911.com suggests using bran as a wheat germ substitute for baked goods because it has a lighter texture and will not weigh down the finished product.
Baking
Many people like to use wheat germ in recipes for bread, muffins, pancakes, waffles or other baked goods to boost their nutritional values and up their fiber contents. If you know that you're using a recipe that simply adds wheat germ for health value, the final product won't suffer in taste or texture if you leave it out. If you do want to keep that component in, however, you can try using ground flaxseed or a finely ground, fiber-rich cereal as a substitute.
Cereal
When you sprinkle wheat germ on your morning cereal, you'll get more of the taste and texture in the product than you will by eating a baked good that has some wheat germ in it. Thus, you may need to substitute differently. Ground seeds, such as sunflower seeds or pumpkin seeds, may add more calories per serving to your cereal, but they have an appealing nutty texture and flavor. You might also consider using whole flaxseeds or crumbled graham crackers.
Alternatives
Although they are more oily and do not produce quite the same texture, ground nuts or nuts that have been pulsed a few times in a food processor add health value to recipes and taste just as good or better than wheat germ when sprinkled on salads, cereal or other dishes. MayoClinic.com recommends adding wheat germ to smoothies, and the nuts can also serve as an adequate substitute there if they are ground finely enough. To keep the final texture smooth, add nut butter instead of crumbled nuts.
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