Fused-silica capillaries for capillary electrophoresis (CE) and gas chromatography (GC) were investigated by atomic force microscopy (AFM). Differences from batch to batch and within one batch were often observed. Surface heterogeneity can be caused by bulk material, manufacturing parameters, or by aging effects. One batch of a fused-silica capillary was stored in water for three years at room temperature. The significant increase in surface roughness (measured as rms = root mean square) during this time is demonstrated. The effect of different drawing temperatures was investigated. Other drawing parameters were kept constant using one capillary batch. If the chosen drawing temperature was too low, the roughness values more than doubled. This increase in roughness did not affect the separation efficiency. However, the relative standard deviation (RSD%) of migration times and peak areas increased at the same time. Three capillary batches for gas chromatography of different inner diameters (250 microm, 320 microm, 530 microm) were also investigated. In all cases the higher rms values for surface roughness could be found at the beginning of the drawing process, although all values were close to atomic flatness.