There are relatively few side effects associated with GBE. Although, mild headaches lasting for a day or two and mild stomach upset have been reported in a very small number of people using GBE.

Ginkgo leaves are known to contain a group of potentially toxic constituents known as alkylphenols. The ginkgo extracts known as EGb 761 and LI 1370 have been shown to conform to the safety limits for these constituents (less that 5 ppm), as set forth by the German Commission E. Other forms of ginkgo may contain higher concentrations of alkylphenols. 

One small clinical trial found that ginkgo supplementation for three months increased secretion of insulin by the pancreas, but did not affect blood glucose levels, in healthy young adults. These results suggest that the participants may have Developed an insensitivity to insulin, a potential concern because insulin insensitivity may be a precursor to type 2 diabetes. However, this trial does not prove that ginkgo causes insulin insensitivity, nor does it prove that long-term Ginkgo supplementation increases the risk for any disease. In addition, the results of this trial are not consistent with other research on ginkgo. Larger and more rigorously designed clinical trials of ginkgo supplementation have found no significant adverse effects after as many as 12 months of supplementation.