Mucinous adenocarcinoma arising in chronic fistula-in-ano is rare, and diagnosing it at an early stage is difficult. The role of endoanal ultrasonography in diagnosing the condition has not been discussed in the study. Herein, we report three cases of mucinous adenocarcinoma arising from anal fistulas in which endosonography played an important role in diagnosing malignant change. Three male patients with a 5- to 20-year history of anal fistula were referred to our hospital due to perianal induration, progressive anal pain, or mucopurulent secretion. In all three patients, endosonography revealed a multiloculated complex echoic mass with isoechoic solid components communicating with a trans-sphincteric fistula and sonography-guided biopsy under anesthesia revealed mucinous adenocarcinoma. All patients underwent abdominoperineal resection with lymph node dissection. One patient with a local recurrence died 3 years after surgery and two have remained disease-free for >6 years. These observations suggest that endosonography may be a reliable technique for the diagnosis of mucinous adenocarcinoma arising from chronic fistula-in-ano. Sonography-guided biopsy is useful for the definitive diagnosis of malignancy. Therefore, periodic endosonography assessment should be recommended for patients with persistent anal fistula, especially those with progressive clinical symptoms. Once malignancy is suspected, aggressive sonography-guided biopsy under anesthesia should be performed, which may enable an early diagnosis, curative treatment, and favorable long-term results.