Occasionally, the secondary opening is closer to the anus than the lowest midline pit. This may then cause confusion with an unrelated condition known as a fistula in ano.
A fistula in ano is a short channel which runs from inside the anus to the nearby skin and clinically may look similar to pilonidal sinus. Importantly, fistula in ano is in no way related to pilonidal sinus.
6% of my patients had a secondary sinus below the midline pits. Rarely, a so-called recurrent pilonidal sinus may actually be a fistula in ano! A recent article reports a middle aged man with what was thought by his surgeon to be a fistula in ano but examination under anaesthesia revealed it to be a pilonidal sinus with a low secondary opening. The surgeon removed the hair and debris from the pilonidal sinus.