Most diet supplements that help users burn fat have some side effects and some may have long term health effects, according to WebMD. The Mayo Clinic explains that supplements do not undergo as thorough testing as prescription drugs prior to being sold.
The supplement chitosan has few side effects, although it may cause upset stomach, according to WebMD. Chromium picolinate is known to cause insomnia, irritability and headaches and has been connected to claims of kidney and liver damage. WebMD suggests people with kidney or liver problems avoid products containing chromium picolinate. Side effects for conjugated linoleic acid may cause loose stool, nausea and an upset stomach.