We studied the influence of extra-pair paternity on heritability estimates of morphological traits in a population of the Medium Ground Finch (Geospizafortis) on Isla Daphne Major, Galápagos. Data from eight microsatellite loci were used to determine parentage. Six morphological traits measured on each finch were represented by two separate principal components analyses, one for the three bill measurements and one for the body size measurements. Heritabilities were calculated using weighted regressions of offspring on their parents and also offspring on their grandparents. We found that 20% of all offspring were extra-pair young but all offspring matched their mothers. Heritabilities derived from midparent–offspring regressions were all high and significantly different from zero. Removing all extra-pair young from the data set increased father–offspring regressions by an average of 21%, but mother–offspring resemblance still exceeded father–offspring resemblance by up to 42%. These results and grandparent–offspring regressions provide evidence for maternal effects, comparable in magnitude to those reported in other studies of wild birds.