The protein family of anion channel (ClC) constitute a family of transmembrane trnsporters that either function as anion channel or as H+/anion exchanger. The expression of three genes of AtClCa, AtClCb and AtClCd in the model plant Arabidopsis thaliana were silenced by a T-DNA insertion . When the pH of the medium was slightly acidic the length of the primary root of plants with a disrupted AtClCa and AtClCd gene was reduced compared to the wild type and the plant with a disrupted AtClCb gene. The proton fluxes and pH were measured along the surface of the root at different positions, from root cap, through the transition zone, and up to the fast elongation zone, and at different pHs of the medium. A high proton influx was found in the apical part of the transition zone. Lower influxes or even small effluxes were found in the basal part of the elongation zone. At pH 6.2 the influx of protons in the apical part of the transition zone in the Atclca and Atclcd mutants was significantly lower than in wildtype and the Atclcb mutant. This will suggest a model for the interaction between endomembrane anion/H+ antiporters, plasma membrane proton fluxes and cell expansion in roots of Arabidopsis.