There is poor correlation between decreases in intraepidermal nerve fiber density (IENFD) and the presence of pain in HIV-associated sensory neuropathy (HIV-SN) and other painful distal symmetrical polyneuropathies. We investigated whether in individuals with HIV-SN, having pain at the ankle skin biopsy site was associated with lower IENFD compared to when there was no pain at the ankle biopsy site. We recruited 15 individuals with symptomatic HIV-SN. Nine had pain at the site where the ankle biopsy was taken, whereas 6 did not. Skin punch biopsies for IENFD quantification were taken from the ankle and the thigh. Contrasts between the 2 groups were made using the overlap of confidence interval (CI) method. Intraepidermal nerve fiber density was substantially lower in the group that had pain at the site of the ankle biopsy compared with the other group (6.6 [CI: 5.3-7.2] vs 3.3 [CI: 10.0-15.0] fibers/mm). However, there was no group differences at the thigh biopsy site (15.6 [CI: 15.0-15.9] vs 16.2 [CI: 14.5-17.8] fibers/mm). When taking the ratio of ankle IENFD:thigh IENFD, the point estimate for the pain at the ankle group (0.43 [CI: 0.36-0.48]) was about half that of the other group (0.81 [CI: 0.68-0.87]). Thus, colocalization of pain to the ankle is associated with meaningful decreases in ankle IENFD.