We have used fountain pen microlithography to deposit arrays of molecularly imprinted polymer microdots on flat substrates. We visualize analyte binding to the dots by fluorescence microscopy with the aid of fluorescein as a model analyte. Elution and readsorption of the analyte to the MIP dots were possible if the porosity of the dots was improved by a sacrificial polymeric porogen. The imprinting effect was confirmed by using compounds structurally related to fluorescein. In addition, we show with another MIP specific to 2,4-D that, apart from the direct measurement of the binding of fluorescent compounds, a competitive immunoassay-type format can also be used to transduce the binding. We believe that this technique has a strong potential for the fabrication of biomimetic microchips and other types of integrated biosensors.