In this study, we introduce a method for estimating the syntactic structure of Japanese speech from F0 contour and pause duration. We defined a prosodic unit (PU) which is divided by the local minimal point of an F0 contour or pause. Combining PUs repeatedly (a pair of PUs is combined into one PU), a tree structure is gradually generated. Which pair of PUs in a sequence of three PUs should be combined is decided by a discriminant function based on the discriminant analysis of a corpus of speech data. We applied the method to the ATR Phonetically Balanced Sentences read by four Japanese speakers. We found that with this method, the correct rate of judgement for each sequence of three PUs is 79% and the estimation accuracy of the entire syntactic structure for each sentence is 26%. We consider this result to demonstrate a good degree of accuracy for the difficult task of estimating syntactic structure only from prosody.