A slip runs from the flexor digitorum longus to the flexor hallucis longus in most individuals, but an additional slip can be viewed as an anatomical variant as well. This extremely rare extra muscle slip is known as the peroneocalcaneus internus, where it originates inferiorly or laterally from the flexor hallucis longus muscle at the back of the fibula and passes over the sustentaculum tali alongside the flexor hallucis tendon inserting into the calcaneus.[3][4]

In patients with an anatomically variable flexor hallucis longus, research has found that the mean distance to the neurovascular tibial bundle increased, as the normal anatomy was 0.9 mm apart while the anatomically varying individuals were 1.3 mm apart. This increased distance helps to improve safety in hindfoot endoscopic procedures.[3]  The anatomical variance between the flexor digitorum longus and flexor hallucis longus muscles in the plantar foot is vital for the facilitation of tendon harvesting; reducing morbidity, and can help explain the possible postoperative functional loss. The slip between the two might also be a reason why the flexion of the lesser toes remains after transferring the flexor digitorum longus muscle.[4]

In terms of a surgical significance, the flexor hallucis longus has a role in Achilles (calcaneal) tendon rupture. A torn Achilles tendon usually presents as a patient reporting a "popping" feeling during strenuous exercise. Achilles tendon ruptures are especially common in patients with intermittent physical activity and are the most common tendon rupture in the lower extremity.[5] Symptoms are weakness and difficulty walking and pain in the heel. Physical exam findings include increased resting ankle dorsiflexion while prone and bent at the knee and calf atrophy in some chronic cases. There usually is a palpable gap on the heel, and the patient will demonstrate a decreased range of motion in ankle plantar flexion and increased passive dorsiflexion. A Thompson test is used to diagnose and presents as a lack of plantar flexion when squeezing the calf.

With the flexor hallucis longus tendon having proximity to the Achilles tendon, the flexor hallucis longus is the most commonly used tendon for tendon transfer when the Achilles tendon is irreparable. The Achilles tendon usually is irreparable on a chronic retracted tear. The combination of its line of pull and proximity make it the ideal candidate for Achilles tendon replacement. The surgical procedure for the flexor hallucis longus tendon replacing the Achilles tendon is called transfer for Achilles reconstruction.[6][7]

A common issue seen with flexor hallucis longus dysfunction is stenosing tenosynovitis, which commonly occurs in ballet dancers that undergo extreme plantarflexion while performing various ballet movements. First line treatment is rest and physical therapy, but if the injury is debilitating enough, a surgical approach is used followed by a well-crafted rehabilitation program. Anti-inflammatory medications can also be prescribed to alleviate symptoms.[8] Diagnosis of stenosing tenosynovitis has proven difficult as many symptoms overlap with flexor hallucis tendinitis, plantar fasciitis, and tarsal tunnel syndrome.[9] 

Hallux saltans is another condition that arises from flexor hallucis longus muscle overuse. A nodule develops along the tendon that can cause a “popping effect” during contraction due to friction with surrounding tissues. If the nodule continues to grow this can cause stenosis of the flexor hallucis longus tendon leading to the stifling of the range of motion in the big toe, leading to relative immobility.[10] When contracted, the appearance of the great toe takes on that of a rigidly flexed interphalangeal joint, a clinical finding known as a checkrein deformity.

Many clinical issues with the flexor hallucis longus muscle and tendon get overlooked because of the muscle being small in size. Diagnosis is via MRI to evaluate the pathology and condition of the flexor hallucis longus tendon. Diagnostic ultrasound is used to evaluate the muscle movement and potential impingement sites.[9][10] 

The flexor hallucis longus tendon also has utility for tendon transfer in chronic calcaneal (Achilles) tendon rupture. Single-incision flexor hallucis longus transfers for calcaneal tendon ruptures are considered a simple method with miniscule morbidity and complications.[6][7]