The isolation of sweat glands from human skin has long been a challenging task. The human scalp contains thousands of eccrine glands, while the axilla harbors both eccrine and apocrine glands. Recently, the close anatomic relationship of the eccrine gland with the scalp hair follicle has been described. Taking advantage of this anatomic relationship, we describe here an efficient method to isolate sweat glands from the human scalp and the axilla using the micro-punch harvesting technique known as follicular unit excision (FUE), commonly employed in hair transplant surgery. Once the follicular unit (FU) has been extracted, it needs to be stained with Methylene Blue or Neutral Red in order to make the sweat gland visible for its dissection under the stereomicroscope. The efficiency of this isolation method should encourage further research into human sweat glands and opens possibilities for new translational applications.