Seed coat integrity of navy beans is extremely important for processing of baked beans. Mechanical damage (MD) of bean seed also causes abnormal emergence and reduced seedling vigor. This prompted an initial study into seed coat integrity, resistance to MD and selection for resistant beans. Our initial study clearly demonstrated variety differences in response to direct combine harvest techniques (2001). The following study was conducted during 2000-01 to determine genetic control of MD, to estimate heritability, and to apply these findings in development of MD tolerant bean cultivars. F4 and F4:5 RIL of two crosses between resistant and susceptible navy beans were tested. The results showed that MD was under quantitative genetic control by multiple minor genes. Heritability estimated by the parent-offspring regression showed moderate heritability of MD (0.55 and 0.65 for two crosses). Correlations between the base population and selected progeny lines suggested that selection for MD tolerance would be moderately effective (r = 0.58 – 0.78) and breeding is possible. Seed characteristics measured by using digital image analysis system found that MD index is highly correlated with some of the seed characteristics like seed length and surface area in one of the two crosses. Some plant and seed characteristics may be used in selecting for resistance to MD. Seed coat tissues were examined by scanning electron microscopy to investigate micro-structural differences of seed coat tissue and the results showed some differences between MD susceptible and resistant parental lines. Air space bellow the parenchyma cells was significantly correlated with MDIc (0.32) as was between lower palisade and MDIs (0.36). Air space between seed coat layers and endosperm might have a cushioning effect to reduce seed coat damage.