Determination of the phase difference between two sinusoidal signals with noise components using samples of these signals is of interest in many measurement systems. The samples of signals are processed by one of many algorithms, such as 7PSF, UQDE and MSAL, to determine the phase difference. The phase difference result must be accompanied with estimation of the measurement uncertainty. The following issues are covered in this paper: the MSAL algorithm background, the ways of treating the bias influence on the phase difference result, comparison of results obtained by applying MSAL and the other mentioned algorithms to the same real signal samples, and evaluation of the uncertainty of the phase difference.