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Although calcaneal speed of sound (SOS) is an effective predictor of osteoporotic fracture risk, clinical SOS measurements exhibit a high degree of inter-system variability. Calcaneal SOS is usually computed from time-of-flight measurements of broadband ultrasound pulses that propagate through the foot. In order to minimize the effects of multi-path interference, many investigators measure time-of-flight from markers near the leading edge of the pulse. The calcaneus is a highly attenuating, highly inhomogeneous bone that distorts propagating ultrasound pulses via frequency-dependent attenuation, reverberation, dispersion, multiple scattering, and refraction. This pulse distortion can produce errors in leading-edge transit-time marker-based SOS measurements. In this paper, an equation to predict dependence of time-domain SOS measurements on system parameters (center frequency and bandwidth), transit-time marker location, and bone properties (attenuation coefficient and thickness) is validated with through-transmission measurements in a bone-mimicking phantom and in 73 women in vivo, using a clinical bone sonometer. In order to test the utility of the formula for suppressing system dependence of SOS measurements, a wideband laboratory data acquisition system was used to make a second set of through-transmission measurements on the phantom. The compensation formula reduced system-dependent leading-edge transit-time marker-based SOS measurements in the phantom from 41 m/s to 5 m/s and reduced average transit-time marker-related SOS variability in 73 women from 40 m/s to 10 m/s. The compensation formula can be used to improve standardization in bone sonometry.