Myoglobin is an important intracellular oxygen transport molecule in muscle. Oxygen binding to myoglobin can be determined spectroscopically due to differences in absorption of oxymyoglobin and deoxymyoglobin. Myoglobin oxygenation can be used as a measure of intracellular oxygen tension in muscle. We sought to determine the effects of differences in temperature and pH on myoglobin absorption spectra in the near-infrared spectral region. Transmission spectra were taken of pure solutions of oxymyoglobin and deoxymyoglobin at 10°, 20°, 30°, and 40°C at pH values of 6.0, 7.0, and 8.0 (n=4). In second derivative spectra at 40°C, the deoxymyoglobin peak near 760 nm was shifted by 0.9-1.2 nm toward longer wavelengths relative to 10°C at constant pH. Differences in pH did not result in statistically significant shifts in this peak at constant temperature. Estimations of myoglobin saturation from myoglobin spectra with intermediate saturations were obtained by least squares (LS) and partial least squares (PLS) analyses. Both algorithms estimate myoglobin saturation with small root mean square errors (<1e-6) when component spectra and calibration set spectra are at the same temperature as test spectra (n=100). However, when spectra at 20°C or 40°C were used as component spectra in LS with test spectra at 30°C (all at pH 7.0), errors were 0.8% and 1.4%, respectively. PLS analysis of 30°C test spectra using 20°C or 40°C calibration set spectra yielded errors of 1.6% and 1.5%, respectively. When the PLS analysis is endpoint corrected, these errors become vanishingly small. These results demonstrate that peak shifts due to temperature are potential sources of error if calibration and test spectra differ by 10°C. These errors can be minimized by appropriate spectral analytic methods.