The purpose of this study was to determine the relationship between stride-to-stride fluctuations and prosthesis preference. Thirteen individuals with unilateral, transtibial amputation consented to participate. Individuals walked on a treadmill for 3 min with their prescribed and an alternate prosthesis. Stride-to-stride fluctuations were quantified with the largest Lyapunov exponent (LyE) of each joint flexion/extension time series. The change in the LyE was calculated for each major lower-limb joint for both conditions. Participants indicated preference between the prostheses on a continuous visual analog scale. The change in the LyE was correlated with the degree of preference between the two prostheses at the prosthetic ankle. The change in the LyE of the prosthetic ankle was strongly related to the degree of preference (r = 0.629, p = 0.02). Thus, stride-to-stride fluctuations, quantified by the LyE, are strongly related to the patient's perception of the prosthesis. As a result, the LyE is the first objective measure to detect changes in gait that relate to the patient's perception of the prosthesis. The LyE should be further examined as a potentially effective prescriptive and outcome measure in prosthetic rehabilitation.