The conventional human tumor stem cell assay is limited by the lack of flexibility for drug scheduling with single agents and its inability to test drug combinations. Recently, we described the cloning of tumor cell lines within porous glass capillary tubes which allow free exchange of substances. The present study describes the influence of various perfusion modalities on the colony growth of the human tumor cell line MDA-231 cloned within the perfused capillary cloning system (PCCS). Colony growth of tumor cells within the PCCS is strongly dependent on perfusion tube volume, flow rate and duration of perfusion with growth medium. Best colony growth was achieved using a perfusion tube volume of 12 ml resulting in a cloning efficiency of 36.3%. Continuous perfusion with fresh medium did not improve the cloning efficiency; in fact, colony growth was hampered compared to colony growth within unperfused porous capillaries. However, cloning efficiency was acceptable when continuous perfusion was started at day 6 (26.4%) instead of day 0 (17.2%), or when a short perfusion with high volume (12 ml/h) was discontinued after 1 h at day 0. In contrast to the conventional capillary cloning system the PCCS has the potential for investigating secretion and kinetics of tumor-specific factors and the effect of growth-stimulating or growth-inhibiting drugs.