Interactions between rice and Magnaporthe oryzae involve the recognition of cellular components and the exchange of complex molecular signals from both partners. How these interactions occur in rice cells is still elusive. We employed robust-long serial analysis of gene expression (RL-SAGE), massively parallel signature sequencing (MPSS), and sequencing by synthesis (SBS), to examine transcriptome profiles of infected rice leaves. A total of 6,413 in-planta expressed fungal genes including 851 genes encoding predicted effector proteins were identified. We used a protoplast transient expression system to assess 42 of the predicted effector proteins for the ability to induce plant cell death. Ectopic expression assays identified five novel effectors that induced host cell death only when they contained the signal peptide for secretion to the extracellular space. The five apoplastic effectors induced cell death in a non-host-selective-manner. Although the five effectors are highly diverse in their sequences, the physiological basis of cell death induced by each was similar. This study demonstrates that our integrative genomic approach is effective for the identification of in-planta expressed cell death-inducing effectors from M. oryzae that may play an important role facilitating colonization and fungal growth during infection.