The presence of less-mature seeds or seeds with cracks in a paddy rice seed lot may result in lower seed quality. The potential of chlorophyll fluorescence to provide information on the maturity of single seeds and X-ray analyses to identify seeds with cracks was evaluated in relation to paddy rice seed quality. Individual seeds from a paddy rice seed lot were classified into fractions on the basis of their level of chlorophyll fluorescence, seed weight, seed area, the presence of cracks and germination behaviour. Seeds from fractions with a high relative level of chlorophyll fluorescence (> 130 units/mm2) were of lower quality. On the basis of the weighted means (i.e. overall mean germination based on proportion of seeds in each fraction), these seeds had slower germination, lower total germination (90%) and fewer normal seedlings (<52%) compared to seeds from fractions with <130 units/mm2 chlorophyll fluorescence (> 96% total germination; 72% normal seedlings). Rice seeds with cracks could be identified using X-ray analysis. The majority of cracked seeds failed to produce a normal seedling, irrespective of the position of the crack. Both chlorophyll fluorescence and X-ray analysis can provide new tools for the fast evaluation of seed lots and may in the future also be used for paddy rice seed sorting.