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Abstract Background Achilles tendinopathy is one of the most common overuse injuries in recreational and competitive runners, yet the clinical significance and frequency of abnormal sonographic characteristics in runners remains unclear. This paper presents a protocol for a systematic review which aims to assess existing literature which has employed ultrasonography to evaluate characteristics of the mid-portion of the Achilles tendon in runners. Methods An electronic literature search will be conducted using the following electronic databases: MEDLINE, CINAHL and SPORTDiscus. Studies published in English will be included if they evaluate ultrasound characteristics associated with mid-portion Achilles tendinopathy in runners. Methodological quality will be assessed using a scale adapted from the Newcastle-Ottawa Scale. Discussion This will be the first systematic review to summarise the existing evidence on ultrasound characteristics of the mid-portion of the Achilles tendon in recreational runners. Systematic review registration PROSPERO CRD42016050509