Genetic variance, phenotypic variance, and the genetic covariance matrix (G) can change as a result of genetic drift. These changes will persist over time to some extent and will continue if population size remains relatively small. Nine populations founded by a single pair of Drosophila melanogaster were measured for a series of six morphological characteristics for a large number of parent-offspring families at both the third generation after the bottlenecks and after 20 generations. From these data, the phenotypic variance, additive genetic variance, and G were estimated for each line at each generation. Phenotypic and genetic variances were highly correlated over time, so that the measurements made at the third generation were predictive of the state of the population 17 generations later. Genetic covariances were also somewhat stable over time; however, the G matrices of some lines changed significantly over the intervening generations. This change did not return the populations toward their original state before the population bottlenecks. We conclude that the genetic covariance matrix can change as a result of mild genetic drift over a short span of time.