A restriction enzyme survey of a 100 kb region including the achaete-scute complex (ASC) examined 14 polymorphic molecular markers in a sample of 56 naturally occurring chromosomes. A permutation test found two polymorphic sites that were independently associated with variation in bristle number among two sets of lines consisting of both extracted X chromosomes and segments of the X chromosome, including the ASC, introgressed into a common background. A six base pair deletion near sca affected sternopleural bristle number in both sexes and a 3.4 kb insertion between scb and scg affected abdominal bristle number in females. Under an additive genetic model, the small deletion polymorphism near sca accounts for 25% of the total X chromosome genetic variation in sternopleural bristle number, and the 3.4 kb insertion accounts for 22% of the total X chromosome variation in female abdominal bristle number. Large insertions as a class were associated with a reduction in both sternopleural and abdominal bristle number. The association of large insertions with variation in bristle number supports deleterious mutation-selection equilibrium models for the maintenance of quantitative genetic variation, whereas the observation of common polymorphisms associated with variation in bristle number are more parsimoniously explained by models which incorporate balancing selection or assume variants affecting bristle number are neutral.