Follicular unit extraction (FUE) generally has a quicker patient recovery time and significantly lower post-operative discomfort than follicular unit transplantation (FUT). FUE provides an alternative to FUT when the scalp is too tight for a strip excision and enables a hair transplant surgeon to harvest finer hair from the nape of the neck to be used at the hairline or for eyebrows.

However, with FUE, the follicles are harvested from a much greater area of the donor zone compared to FUT, estimated to be eight times greater than that of traditional strip excision so requires patients to have hairs trimmed in a much larger donor area.As a result, the hair in the lower and upper parts of the donor area, where the grafts were taken from, may thin and this can make the donor scars visible.

Follicles harvested from borderline areas of the donor region may not be truly “permanent,” so that over time, the transplanted hair may be lost. Maximum follicular unit graft yield is lower than with FUT and may result in greater follicular transection (damage).

Due to the scarring and distortion of the donor scalp from FUE it makes subsequent sessions more difficult, and grafts are more fragile and subject to trauma during placing, since they often lack the protective dermis and fat of microscopically dissected grafts,ultimately which may result in poor growth. A problem of buried grafts can occur during the blunt phase of the three-step technique when the graft is pushed into fat and must be removed through a small incision. FUE can also be more expensive and take longer to perform than FUT, so grafts are usually out of the body longer, risking sub-optimal growth.