Somatic embryogenesis is an important biotechnological tool in breeding and conservation programmes for woody species. It exists an increasing interest in the improvement of somatic embryogenesis induction in commercial species such as Pinus radiata. One approach to obtain markers of successful somatic embryogenesis can be the study of protein profiling in a descriptive study. In order to accomplish this objective, 2-D and MALDI-TOF/TOF-MS analysis were used in the identification and quantification of proteins from Pinus radiata D. Don somatic embryos derived from 4 cell lines that were generated under different environmental conditions at initiation stage. Based on the Swiss-Prot database, among the 139 proteins detected, 25 of them appeared only in those cell lines with low initiation percentage at the initial stage of somatic embryogenesis. Only two proteins were detected differentially in cell lines with high initiation rates. Approximately 60% of the proteins identified were related to carbohydrate metabolic process and defence response. This study gives new insights about the proteomics in forest trees, as well as provides clues on the underlying causes of the mechanisms governing Pinus radiata somatic embryogenesis process, and can serve as a tool for facing the improvement ofthe breeding programmes.