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Ultrasound biomicroscopy (UBM) is a non-invasive imaging technique used in examination of several skin diseases but never in imaging hair and scalp diseases. Main objective of this investigation was assessment of the efficacy of UBM for in vivo visualization of hair follicles in cases of alopecia areata (AA) and correlation of findings with histopathological findings. This study included 30 patients with AA. Two areas, one with AA and a control area, were marked, examined by UBM and then biopsied for histopathological examination. In patients with alopecia totalis (AT) or universalis (AU) only an AA area was examined. Non-echogenic conical shadows reaching the epidermal entrance echo (probably corresponding to the hair follicles) were seen and were wider and fewer in number in areas of AA than in normal control areas. No significant difference was found regarding number and width of hair follicles between UBM and histopathological examination. However, a significant increase in length of follicles in histopathology was detected, indicating that the UBM image was probably unable to reach the deepest part of the follicle. Main limitation of the study is small number of cases. No significant difference was found between UBM and histological measurements of hair follicle number and width in patients with AA, making UBM a useful tool for in vivo visualization of hair follicles.