The study compared the protein differences between self- and across-pollinated self-incompatible (SI) apricots by two-dimensional gel electrophoresis and liquid chromatography-electrospray ion trap tandem mass spectrometry, the results showed that nine protein spots were expressed in self-pollinated pistil and only one was expressed in cross-pollinated pistils. Sixteen and three protein spots were up- and down-regulated in cross-pollinated pistils, respectively, compared with self-pollinated pistils. Seven protein spots were identified unambiguously by SEQUEST in NCBI protein database: Actin-12, enolase, MYB transcription-factor-like protein, heat-shock protein 70 were upregulated in cross-pollinated pistils compared with self-pollinated pistils; and actin-7, actin-8 and fructose bisphosphate aldolase-like protein were detected only in self-pollinated pistils.