Validation of marker-QTL association for genes grain size 3 (GS3), grain weight 2 (GW2), seed width 5 (qSW5) and a QTL qgrl7.1 for grain length was undertaken in a set of 242 diverse rice germplasm. Further, the study was extended to an F2 mapping population derived from cross of Sonasal, a short grain aromatic rice landrace with Pusa Basmati 1121, a variety with extra long slender grains. Seven gene specific markers, namely, SF28, SR17, RGS1and RGS2 based on GS3, W004 for GW2, MS40671 for qSW5 and RM505 for qgrl7.1, were used for validation. Single marker analysis revealed significant association of these markers to grain size and shape. The marker SF28 explained highest phenotypic variance (37 %) while the marker W004 explained lowest variance (2.6 %) for grain length in the germplasm set at the significance level P < 0.05. Three markers namely, SF28, MS40671 and RM505 were polymorphic between the parents Sonasal and Pusa Basmati 1121. In the F2 population, the marker SF28 linked to gene GS3 explained highest phenotypic variance (32.5 %), while RM505 linked to qgrl7.1 explained 5.4 % of phenotypic variance for grain length. The marker SF28 was found to be most robust in the validation studies both in germplasm and F2 population. The validated gene specific markers can be utilised in marker assisted selection for improving grain size and shape as these traits have significant contribution towards grain quality and grain yield. This is the first study on validation of gene based markers for grain dimension traits in Indian rice germplasm. © 2012 Society for Plant Biochemistry and Biotechnology.