Asymptomatic pilonidal sinus disease (PSD) discovered incidentally is regarded as a precursor of symptomatic disease, which is characterized by intradermal hair eliciting an inflammatory reaction. We aimed to investigate whether asymptomatic PSD already shows inflammation, though clinically inapparent, or represents a ‘virgin’ sinus. One thousand seven hundred and thirty-one medical records of patients presenting with primary PSD, which underwent surgery, were analysed to identify patients with surgically resected incidental PSD. Acute purulent pilonidal disease was seen in 514 of 1,731, whereas chronic fistulating pilonidal disease was the most common diagnosis group with 1,019 of 1,731 (58.9%). One hundred and forty-three of 1,731 (8.3%) patients had a previous chronic remitting pilonidal sinus. A total of 55 (3.2%) patients with clinically asymptomatic PSD were identified. Histological workup documented hair in 64.6% (1,119/1,731), with comparable rates between 68% and 71% in chronic fistulating disease, chronic remitting disease and incidental PSD (p = 0.80). Inflammation was found in 53 of 55 (96.4%) incidental PSD specimens, with two thirds (37 of 55) showing chronic inflammatory changes and one third (16 of 55) combining acute and chronic inflammation. Our findings support the idea that incidental PSD is a sub-clinically inflamed pilonidal sinus, with hair and chronic infection present. However, the data suggest that a prophylactic surgery for asymptomatic PSD provides no benefit for the patient compared to surgery in chronic PSD; thus, observational treatment is most likely sufficient for asymptomatic PSD.