Purpose To compare the acoustic measurements of Cepstral Peak Prominence Smoothed (CPPS) and Acoustic Voice Quality Index (AVQI) of children with normal and altered voices, to relationship with auditory-perceptual judgment (APJ) and to establish cut-off points. Methods Vocal recordings of the sustained vowel and number counting tasks of 185 children were selected from a database and submitted to acoustic analysis with extraction of CPPS and AVQI measurements, and to APJ. The APJ was performed individually for each task, classified as normal or altered, and for the tasks together defining whether the child would pass or fail in a situation of vocal screening. Results Children with altered APJ and who failed the screening had lower CPPS values and higher AVQI values, than those with normal APJ and who passed the screening. The APJ of the sustained vowel task was related to CPPS and AVQI, and APJ of the number counting task was related only to AVQI and CPPS numbers. The cut-off points that differentiate children with and without vocal deviation are 14.07 for the vowel CPPS, 7.62 for the CPPS numbers and 2.01 for the AVQI. Conclusion Children with altered voices, have higher AVQI values and lower CPPS values, when detected in children with voices within the normal range. The acoustic measurements were related to the auditory perceptual judgment of vocal quality in the sustained vowel task, however, the number counting task was related only to the AVQI and CPPS. The cut-off points that differentiate children with and without vocal deviation are 14.07 for the CPPS vowel, 7.62 for the CPPS numbers and 2.01 for the AVQI. The three measures were similar in identifying voices without deviation and dysphonic voices.