Background Measuring the strength of individual foot muscles is very challenging; however, measuring muscle morphology has been shown to be associated with strength. A reliable method of assessing foot muscle atrophy and hypertrophy would therefore be beneficial to researchers and clinicians. Thus, the aim of this study was to evaluate the test-retest intra-observer reliability of ultrasound to measure the morphology of the primary toe flexor muscles. Method The abductor hallucis, flexor hallucis brevis, flexor digitorum brevis, quadratus plantae and abductor digiti minimi muscles in the foot, and the flexor digitorum longus and flexor hallucis longus muscles in the shank were assessed in five males and five females (mean age = 32.1 +/- 10.1 years). Muscles were imaged using a GE Venue 40 ultrasound (6--9 or 7.6-10.7 MHz transducer) in a random order, and on two occasions 1--6 days apart. Muscle thickness and cross-sectional area were measured using Image J software with the assessor blinded to muscle and day of scan. Intraclass correlation coefficients (ICC) and limits of agreement were calculated to assess day-to-day repeatability of the measurements. Results The method was found to have good reliability (ICC = 0.89-0.99) with limits of agreement between 8-28% of the relative muscle size. Conclusion The protocol described in this paper showed that ultrasound is a reliable method to measure morphology of the toe flexor muscles. The portability and advantages of ultrasound make it a useful tool for clinical and research settings.