A low lying peroneus brevis muscle belly is a rare anomaly. There are few published studies that support presence of this anomaly as an etiology for peroneal tendon tear. However, the association between a low lying peroneus muscle belly (LLMB) and tendon subluxation is not well explored. In this retrospective study, the magnetic resonance imaging (MRI) and intraoperative findings of 50 consecutive patients undergoing a primary peroneal tendon surgery, in a five year period, were assessed. The sensitivity and specificity of MRI, in comparison to intraoperative findings for identifying peroneal tendon disease was investigated. Presence of associated peroneal tendon pathologies in patients with and without LLMB was compared. Sensitivity of MRI was high in identifying peroneal tenosynovitis (81.58%) and tear (85.71%). Although the sensitivity of MRI for detecting a LLMB (3.23%) and tendon subluxation (10.00%) was low, MRI had high specificity at 94.74% and 100%, respectively. Intraoperatively, LLMB was seen in 62.00% of patients with chronic lateral ankle pain and was associated with 64.52% cases of tenosynovitis, 29.03% cases of tendon subluxation, and 80.65% cases of peroneus brevis tendon tear. While presence of a LLMB did not show any statistically significant association with peroneus brevis tendon subluxation, among the 10 patients with intraoperatively observed tendon subluxation, 9 had a concomitant LLMB. More studies with a larger patient population are needed to better study the role of a low lying muscle belly as a mass occupying lesion resulting in peroneal tendon subluxation.