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Dipstick-based urinalysis is routinely used for detection of early signs of such pregnancy complications, as preeclampsia and gestational diabetes. Usually it is done in doctor’s office using an automatic dipstick analyzer. Here we present a novel smartphone-based colorimeter and demonstrate its application to the measurements of glucose and protein concentrations in biological samples. The key innovations of our approach was to combine powerful image processing encoded into a mobile phone application with a low cost 3D printed sample holder that allowed to control lighting conditions and significantly improved sensitivity. Different solutions with protein and glucose concentrations ranging from 0 to 2000 mg/dL were prepared and analyzed using our system. The smartphone-based colorimeter always correctly classified the corresponding reagent strip pads, what confirms that it can be used as a low cost alternative for commercial dipstick analyzers.