The use of glass-silicon chips for PCR analysis has been widely reported in the last decade, but there have been few systematic efforts to pin down the biochemical problems such systems bring forth. Here we report a systematic analysis of material-related inhibition and adsorption phenomena in glass-silicon PCR-chips. The results suggest that the previously reported inhibition of PCR by silicon-related materials stems mainly from the adsorption of Taq polymerase at chip walls due to increased surface-to-volume ratios, and not from a straight chemical action of silicon-related materials on the PCR-mix. In contrast to Taq polymerase, DNA is not adsorbed in noticeable amounts. The net effect of polymerase adsorption can be counteracted by the addition of a titrated amount of competing protein bovine serum albumin (BSA) and the ensuing reactions can be kinetically optimized in chips to yield effective amplifications in the whereabouts of 20 min.