Stomata are consistently patterned so that they are not in contact. This patterning is violated in the too many mouths (tmm) and four lips (flp) mutations of Arabidopsis thaliana (L.) Heynh. which have stomatal clusters in the first-formed leaves. To clarify the function of both genes in stomatal initiation and patterning, the phenotypes of many different organs were quantified. The flp mutation affects dorsiventral and cylindrical organs differentially with respect to the frequency of clustering. The tmm mutation has a more complex region-specific phenotype in that some regions lack stomata entirely, other regions have excess stomata, and the flower stalk exhibits an apex-to-base gradient from excess to no stomata. This suggests that TMM represents an unusual type of gene regulating plant cell development in that it can either influence stomatal initiation in a positive or negative fashion depending on region. Since the frequencies of initiation and clustering can be uncoupled in tmm, these two functions are under separate region-specific control. Analysis of double mutants shows that tmm and flp in some cases show region-specific interactions in both cluster formation and initiation, and that there may be subpopulations of stomata under different genetic control.