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Hydrophobic sol–gel derived methylsilsesquioxane (MSQ) was compared to wax and alkylketene dimer (AKD) as barrier materials defining channels in paper-based microfluidic devices. While all three of the barrier types performed well with water, only the MSQ barriers were not breached by aggressive cell lysing solutions and surfactant solutions (SDS, CTAB, Triton X-100). The MSQ barriers also withstood glycerol, toluene and DMSO whereas all three barrier types were breached by alcohols. MSQ based devices could be prepared either by direct inkjet printing of the barriers or by base etching of MSQ impregnated paper. The functionality of MSQ based devices was demonstrated by formatting a colormetric sensor for Escherichia coli.