Cold neutral atoms can be controlled and manipulated in microscopic potentials near surfaces of atom chips. These integrated micro-devices combine the known techniques of atom optics with the capabilities of well established micro-and nanofabrication technology. This approach is well suited to explore the realm of mesoscopic matter wave physics. In our experiments, we are able to investigate a variety of phenomena, ranging from quantum gases in low dimensional confinement to quantum control and manipulation of small ensembles or even single atoms.We use current and charge carrying structures to form complex potentials with high spatial resolution only microns from the surface. Here, we will give an overview of our experiments studying the manipulation of both thermal atoms and Bose-Einstein condensates (BEC) on atom chips. In particular, atoms can be confined to an essentially one-dimensional motion, i.e. the temperature of a cloud can be smaller than the transverse energy level spacing of the potential. In the case of a BEC, the transverse ground state energy can exceed the chemical potential of the BEC. First experiments in this quasi one-dimensional regime will be presented. These experiments are only possible because residual disorder potentials caused by imperfections of the chip fabrication are strongly reduced with respect to previously published experiments. This is due to our purely lithographic fabrication technique that proves to be advantageous over electroplating. We have used one dimensionally confined BECs as an ultra-sensitive probe to characterize these potentials in detail.An important application of BECs in extremely elongated traps that can be placed at virtually arbitrary positions near a variety of surfaces is high sensitivity, high resolution metrology, in particular of magnetic fields. We show how a magnetic microscope can be based on BECs confined in chip based microtraps. The technique proves to be competitive with conventional devices and further development is likely to surpass the sensitivity limits of today's state of the art sensors.The smooth potentials allow us to explore various aspects of the physics of degenerate quantum gases in low dimensions. In this context, we will present experiments investigating and comparing the formation of condensates in one and three dimensions and the intermediate crossover regime. In addition, we have started to explore transport processes of one dimensionally confined condensates.Recent experiments have shown that optical cavities can be used to detect small ensembles of atoms containing merely 10 atoms or less even with moderate cavity finesses of 100. Micro cavities reaching appropriate parameters have now been integrated on atom chips, and we will report on the progress of experiments aiming at the detection of very small ensembles or even single atoms in chip traps and guides using this technique. 0-7803-8973