Our understanding of pilonidal sinus disease (PSD) is based on a paper published 29 years ago by Karydakis. Since then, surgeons have been taught that hair more easily penetrates wet skin, leading to the assumption that sweating promotes PSD. This postulate, however, has never been proven. Thus we used pilocarpine iontophoresis to assess sweating in the glabella sacralis. 100 patients treated for PSD and 100 controls were matched for sex, age and body mass index (BMI). Pilocarpine iontophoresis was performed for 5 min, followed by 15 min of sweat collection. PSD patients sweated less than their matched pairs (18.4 ± 1.6 µl vs. 24.2 ± 2.1 µl, p = 0.03). Men sweated more than women (22.2 ± 1.2 µl vs. 15.0 ± 1.0 µl in non-PSD patients (p < 0.0001) and 20.0 ± 1.9 µl vs. 11.9 ± 2.0 µl in PSD patients (p = 0.051)). And regular exercisers sweated more than non-exercisers (29.1 ± 2.9 µl vs. 18.5 ± 1.6 µl, p = 0.0006 for men and 20.7 ± 2.3 µl vs. 11.4 ± 1.4 µl, p = 0.0005 for women). PSD patients sweat less than matched controls. Thus sweating may have a protective effect in PSD rather than being a risk factor.