Background Due to complexity of the plantar intrinsic foot muscles, little is known about their muscle architecture in vivo. Chronic plantar fasciitis may be accompanied by muscle atrophy of plantar intrinsic foot muscles and tibialis posterior compromising the dynamic support of the foot prolonging the injury. Magnetic resonance images of the foot may be digitized to quantify muscle architecture. The first purpose of this study was to estimate in vivo the volume and distribution of healthy plantar intrinsic foot muscles. The second purpose was to determine whether chronic plantar fasciitis is accompanied by atrophy of plantar intrinsic foot muscles and tibialis posterior. Methods Magnetic resonance images were taken bilaterally in eight subjects with unilateral plantar fasciitis. Muscle perimeters were digitally outlined and muscle signal intensity thresholds were determined for each image for volume computation. Findings The mean volume of contractile tissue in healthy plantar intrinsic foot muscles was 113.3 cm3. Forefoot volumes of plantar fasciitis plantar intrinsic foot muscles were 5.2% smaller than healthy feet (P = 0.03, ES = 0.26), but rearfoot (P = 0.26, ES = 0.08) and total foot volumes (P = 0.07) were similar. No differences were observed in tibialis posterior size. Interpretations While the total volume of plantar intrinsic foot muscles was similar in healthy and plantar fasciitis feet, atrophy of the forefoot plantar intrinsic foot muscles may contribute to plantar fasciitis by destabilizing the medial longitudinal arch. These results suggest that magnetic resonance imaging measures may be useful in understanding the etiology and rehabilitation of chronic plantar fasciitis.