To investigate the use of photoacoustic (PA) spectrum analysis (PASA) to identify microstructural changes corresponding to fat accumulation in mouse livers ex vivo and in situ.The laboratory animal protocol for this work was approved by the university committee on use and care of animals. Six mice with normal livers and six mice with fatty livers were examined ex vivo with a PA system at 1200 nm, and nine similar pairs of mice were examined at 532 nm. To explore the feasibility of this technique for future study in an in vivo mouse model, an additional pair of normal and fatty mouse livers was scanned in situ with an ultrasonographic (US) and PA dual-modality imaging system. The PA signals acquired were analyzed by using the proposed PASA method. Results of the groups were compared by using the Student t test.Prominent differences between the PASA parameters from the fatty and normal mouse livers were observed. The analysis of the PASA parameters from six normal and six fatty mouse livers indicates that there are differences of up to 5 standard deviations between the PASA parameters of the normal livers and those of the fatty livers at 1200 nm; for parameters from nine normal and nine fatty mouse livers at 532 nm, the differences were approximately 2 standard deviations (P < .05) for each PASA parameter.The results supported our hypothesis that the PASA allows quantitative identification of the microstructural changes that differentiate normal from fatty livers. Compared with that at 532 nm, PASA at 1200 nm is more reliable for fatty liver diagnosis. Online supplemental material is available for this article.