This paper presents a method for quantitatively estimating intonation variation in Mandarin speech. Intonation variation is relative to identical lexical tone structures, and its estimation is performed on two sets of fundamental frequency ( ) contours: one for norms and the other as variants. This is done by transforming target values in pairs from the norms to the variants in which the prosodic contribution to these contours is analyzed as sequences of targets, all of which are confined to the basic elements of the underlying lexical tone structures. The tone transformations are constrained under an assumption of the structural formulation of contours proposed previously. When the norms take the base values of the four lexical tones measured from isolated words in a neutral mood and voice, this method solves acoustic correlations of tone and intonation from the observed contours. The method was implemented on a computer, and its capability of estimating intonation variation was shown through the analysis and synthesis of contours.