MDVP and Praat are computer programs commonly used for acoustic analysis of voice in clinical and research settings. Both softwares extract a set of acoustic parameters, many of which are defined similarly. The purpose of the present study was to compare the results obtained by both programs, and examine whether they can clinically distinguish among pathological groups differently than the other. Fifty-eight women participated in the study. Of these women, 28 were diagnosed with functional dysphonia and 30 women were diagnosed with benign mass-lesions (ten nodules, ten polyps and ten cysts). Voice samples, which consisted of six productions of the vowels /a/ and /i/, were analyzed using MDVP and Praat. Results show similar mean fundamental-frequency (mF0) values for both programs (P>0.05). However, jitter, shimmer, Noise-to-harmonic ratio (NHR) and degree of unvoiced (DUV) were significantly lower using Praat, in comparison with MDVP. High correlation coefficients were found between the parallel pairs of acoustic parameters extracted by the two programs. Jitter values obtained using MDVP, for the vowel /i/, revealed a significant group difference between the nodule and cyst groups (P<0.05). This group contrast was not observed using Praat. Results suggest that although high correlations are found between values obtained by both programs, individual numerical values vary greatly. Therefore, combining results from both programs is not advisable. In addition, there are indications that linear transformation for the results from one program to the other might lead to erroneous conclusions, and should be carried out with caution.