To investigate the proteome during embryonic development of honeybees, Apis mellifera, proteins were identified by two-dimensional gel electrophoresis, mass spectrometry and protein engine identification tools that were applied to MASCOT and Xproteo search engines. 312, 320, 315 proteins were detected in 24, 48 and 72 h embryos. Thirty-eight highly abundant proteins were identified at the three time points by MS fingerprinting. All 21 proteins could be identified as products of annotated genes of the honeybee. Identified proteins included six proteins related to the metabolism of carbohydrates and energy production, six proteins belonging to the heat shock protein family, three cytoskeletal proteins, four proteins related to the antioxidant system of the embryo and two proteins related to growth regulation of the embryo. Quantitative proteomics was applied to analyze differences in amounts of these proteins during the three above mentioned developmental stages. Our data present an initial molecular picture of honeybee embryos, and will hopefully pave the way for future research on this animal.