Quantitative information on yield losses is vital to the development of sound management strategies for rice diseases. The difference between attainable and actual yield represent the loss due to yield reducing factors of diseases, pests, weeds and calamities. Chronic (brown spot), sporadic but potentially devastating (blast, bacterial blight) and diseases negatively associated with higher attainable yields (sheath blight, false smut) are known to reduce yields up to 10% in different seasons and years. Identification and deployment of qualitative and quantitative resistance to major diseases like blast and bacterial blight and gene/QTL discovery for resistance to diseases such as sheath blight are major challenges. Marker assisted selection/marker assisted backcross breeding has led to the development and releases of a number of improved rice varieties against blast and bacterial blight in the recent past. With the evolution of new races/biotypes it has become necessary to develop broad spectrum, race non-specific resistance to combat the evolution of new virulence. Rice breeding programmes targeting sophisticated signalling pathways against invasion by pathogens, high throughput genotyping associated with large breeding populations for multiple stress tolerance, focused breeding programs involving multi-parent advanced generation inter-crosses (MAGIC) and gene editing technologies are offering new avenues to gene deployment. This paper summarizes achievements in molecular breeding using marker-aided selection and marker assisted backcross breeding (MAS/MABB), and highlights application of new genomic tools to find and deploy novel genes for resistance to multiple diseases.