When toenail thickening occurs in younger people it is most commonly due to infection or injury. If the thickening is caused by toenail fungus, the nail may turn a yellow or brown color before it begins to thicken. Fungal infections often have a foul odor, and may cause fluid to collect under the nail. Trauma, whether caused by he dropping of a hammer on the toe or by the imperceptible pressure of a shoe, can result in permanent thickening of the nail. 2  Systemic diseases such as psoriasis, eczema, rheumatoid arthritis, cardiovascular disease, and cancer, to name a few, may affect the toenails.